diff --git a/Data/Sys/Shaders/Anaglyph/dubois.glsl b/Data/Sys/Shaders/Anaglyph/dubois.glsl
new file mode 100644
index 0000000000..66f9e8382f
--- /dev/null
+++ b/Data/Sys/Shaders/Anaglyph/dubois.glsl
@@ -0,0 +1,18 @@
+// Anaglyph Red-Cyan shader based on Dubois algorithm
+// Constants taken from the paper:
+// "Conversion of a Stereo Pair to Anaglyph with
+// the Least-Squares Projection Method"
+// Eric Dubois, March 2009
+
+void main()
+{
+	float4 c0 = SampleLayer(0);
+	float4 c1 = SampleLayer(1);
+	mat3 l = mat3( 0.437, 0.449, 0.164,
+	              -0.062,-0.062,-0.024,
+	              -0.048,-0.050,-0.017);
+	mat3 r = mat3(-0.011,-0.032,-0.007,
+	               0.377, 0.761, 0.009,
+	              -0.026,-0.093, 1.234);
+	SetOutput(float4(c0.rgb * l + c1.rgb * r, c0.a));
+}
diff --git a/Data/Sys/Shaders/Anaglyph/fullcolor.glsl b/Data/Sys/Shaders/Anaglyph/fullcolor.glsl
new file mode 100644
index 0000000000..8f033aedf1
--- /dev/null
+++ b/Data/Sys/Shaders/Anaglyph/fullcolor.glsl
@@ -0,0 +1,8 @@
+// Anaglyph Red-Cyan shader without compensation
+
+void main()
+{
+	float4 c0 = SampleLayer(0);
+	float4 c1 = SampleLayer(1);
+	SetOutput(float4(c0.r, c1.gb, c0.a));
+}
diff --git a/Data/Sys/Shaders/Anaglyph/grayscale.glsl b/Data/Sys/Shaders/Anaglyph/grayscale.glsl
new file mode 100644
index 0000000000..a1be73da28
--- /dev/null
+++ b/Data/Sys/Shaders/Anaglyph/grayscale.glsl
@@ -0,0 +1,10 @@
+// Anaglyph Red-Cyan grayscale shader
+
+void main()
+{
+	float4 c0 = SampleLayer(0);
+	float avg0 = (c0.r + c0.g + c0.b) / 3.0;
+	float4 c1 = SampleLayer(1);
+	float avg1 = (c1.r + c1.g + c1.b) / 3.0;
+	SetOutput(float4(avg0, avg1, avg1, c0.a));
+}
diff --git a/Data/Sys/Shaders/Anaglyph/grayscale2.glsl b/Data/Sys/Shaders/Anaglyph/grayscale2.glsl
new file mode 100644
index 0000000000..1746396fd8
--- /dev/null
+++ b/Data/Sys/Shaders/Anaglyph/grayscale2.glsl
@@ -0,0 +1,12 @@
+// Anaglyph Red-Cyan luma grayscale shader
+// Info: http://www.oreillynet.com/cs/user/view/cs_msg/8691
+
+void main()
+{
+	float3 luma = float3(0.222, 0.707, 0.071);
+	float4 c0 = SampleLayer(0);
+	float avg0 = dot(c0.rgb, luma);
+	float4 c1 = SampleLayer(1);
+	float avg1 = dot(c1.rgb, luma);
+	SetOutput(float4(avg0, avg1, avg1, c0.a));
+}
diff --git a/Source/Core/Common/CommonPaths.h b/Source/Core/Common/CommonPaths.h
index 62d0ea3db3..4292befa9a 100644
--- a/Source/Core/Common/CommonPaths.h
+++ b/Source/Core/Common/CommonPaths.h
@@ -74,6 +74,7 @@
 #define WII_SYSCONF_DIR     "shared2" DIR_SEP "sys"
 #define WII_WC24CONF_DIR    "shared2" DIR_SEP "wc24"
 #define THEMES_DIR          "Themes"
+#define ANAGLYPH_DIR        "Anaglyph"
 
 // Filenames
 // Files in the directory returned by GetUserPath(D_CONFIG_IDX)
diff --git a/Source/Core/DolphinWX/VideoConfigDiag.cpp b/Source/Core/DolphinWX/VideoConfigDiag.cpp
index 93cf7b1078..09d0aa9d1d 100644
--- a/Source/Core/DolphinWX/VideoConfigDiag.cpp
+++ b/Source/Core/DolphinWX/VideoConfigDiag.cpp
@@ -395,29 +395,14 @@ VideoConfigDiag::VideoConfigDiag(wxWindow* parent, const std::string &title, con
 	}
 
 	// postproc shader
-	if (vconfig.backend_info.PPShaders.size())
+	if (vconfig.backend_info.bSupportsPostProcessing)
 	{
 		wxFlexGridSizer* const szr_pp = new wxFlexGridSizer(3, 5, 5);
 		choice_ppshader = new wxChoice(page_enh, wxID_ANY);
 		RegisterControl(choice_ppshader, wxGetTranslation(ppshader_desc));
-		choice_ppshader->AppendString(_("(off)"));
-
 		button_config_pp = new wxButton(page_enh, wxID_ANY, _("Config"));
 
-		for (const std::string& shader : vconfig.backend_info.PPShaders)
-		{
-			choice_ppshader->AppendString(StrToWxStr(shader));
-		}
-
-		if (vconfig.sPostProcessingShader.empty() || vconfig.iStereoMode == STEREO_ANAGLYPH)
-			choice_ppshader->Select(0);
-		else
-			choice_ppshader->SetStringSelection(StrToWxStr(vconfig.sPostProcessingShader));
-
-		// Should the configuration button be loaded by default?
-		PostProcessingShaderConfiguration postprocessing_shader;
-		postprocessing_shader.LoadShader(vconfig.sPostProcessingShader);
-		button_config_pp->Enable(postprocessing_shader.HasOptions());
+		PopulatePostProcessingShaders();
 
 		choice_ppshader->Bind(wxEVT_CHOICE, &VideoConfigDiag::Event_PPShader, this);
 		button_config_pp->Bind(wxEVT_BUTTON, &VideoConfigDiag::Event_ConfigurePPShader, this);
@@ -745,3 +730,36 @@ void VideoConfigDiag::CreateDescriptionArea(wxPanel* const page, wxBoxSizer* con
 	// Store description text object for later lookup
 	desc_texts.insert(std::pair<wxWindow*,wxStaticText*>(page, desc_text));
 }
+
+void VideoConfigDiag::PopulatePostProcessingShaders()
+{
+	std::vector<std::string> &shaders = (vconfig.iStereoMode == STEREO_ANAGLYPH) ?
+			vconfig.backend_info.AnaglyphShaders : vconfig.backend_info.PPShaders;
+
+	if (shaders.empty())
+		return;
+
+	if (vconfig.iStereoMode != STEREO_ANAGLYPH)
+		choice_ppshader->AppendString(_("(off)"));
+
+	for (const std::string& shader : shaders)
+	{
+		choice_ppshader->AppendString(StrToWxStr(shader));
+	}
+
+	if (!choice_ppshader->SetStringSelection(StrToWxStr(vconfig.sPostProcessingShader)))
+	{
+		// Invalid shader, reset it to default
+		choice_ppshader->Select(0);
+
+		if (vconfig.iStereoMode == STEREO_ANAGLYPH)
+			vconfig.sPostProcessingShader = shaders[0];
+		else
+			vconfig.sPostProcessingShader.clear();
+	}
+
+	// Should the configuration button be loaded by default?
+	PostProcessingShaderConfiguration postprocessing_shader;
+	postprocessing_shader.LoadShader(vconfig.sPostProcessingShader);
+	button_config_pp->Enable(postprocessing_shader.HasOptions());
+}
diff --git a/Source/Core/DolphinWX/VideoConfigDiag.h b/Source/Core/DolphinWX/VideoConfigDiag.h
index d3224d9e2a..10eb8c0385 100644
--- a/Source/Core/DolphinWX/VideoConfigDiag.h
+++ b/Source/Core/DolphinWX/VideoConfigDiag.h
@@ -144,7 +144,7 @@ protected:
 	void Event_PPShader(wxCommandEvent &ev)
 	{
 		const int sel = ev.GetInt();
-		if (sel)
+		if (sel || vconfig.iStereoMode == STEREO_ANAGLYPH)
 			vconfig.sPostProcessingShader = WxStrToStr(ev.GetString());
 		else
 			vconfig.sPostProcessingShader.clear();
@@ -152,7 +152,7 @@ protected:
 		// Should we enable the configuration button?
 		PostProcessingShaderConfiguration postprocessing_shader;
 		postprocessing_shader.LoadShader(vconfig.sPostProcessingShader);
-		button_config_pp->Enable(postprocessing_shader.HasOptions() && vconfig.iStereoMode != STEREO_ANAGLYPH);
+		button_config_pp->Enable(postprocessing_shader.HasOptions());
 
 		ev.Skip();
 	}
@@ -181,15 +181,10 @@ protected:
 
 	void Event_StereoMode(wxCommandEvent &ev)
 	{
-		if (ev.GetInt() == STEREO_ANAGLYPH && vconfig.backend_info.PPShaders.size())
+		if (vconfig.backend_info.bSupportsPostProcessing)
 		{
 			// Anaglyph overrides post-processing shaders
-			choice_ppshader->Select(0);
-			choice_ppshader->Enable(false);
-		}
-		else if (vconfig.backend_info.PPShaders.size())
-		{
-			choice_ppshader->Enable(true);
+			choice_ppshader->Clear();
 		}
 
 		ev.Skip();
@@ -214,6 +209,10 @@ protected:
 		virtual_xfb->Enable(vconfig.bUseXFB);
 		real_xfb->Enable(vconfig.bUseXFB);
 
+		// Repopulating the post-processing shaders can't be done from an event
+		if (choice_ppshader && choice_ppshader->IsEmpty())
+			PopulatePostProcessingShaders();
+
 		// Things which shouldn't be changed during emulation
 		if (Core::IsRunning())
 		{
@@ -251,6 +250,7 @@ protected:
 	void Evt_EnterControl(wxMouseEvent& ev);
 	void Evt_LeaveControl(wxMouseEvent& ev);
 	void CreateDescriptionArea(wxPanel* const page, wxBoxSizer* const sizer);
+	void PopulatePostProcessingShaders();
 
 	wxChoice* choice_backend;
 	wxChoice* choice_adapter;
diff --git a/Source/Core/UICommon/UICommon.cpp b/Source/Core/UICommon/UICommon.cpp
index 8e260f582d..735487306a 100644
--- a/Source/Core/UICommon/UICommon.cpp
+++ b/Source/Core/UICommon/UICommon.cpp
@@ -65,6 +65,7 @@ void CreateDirectories()
 	File::CreateFullPath(File::GetUserPath(D_MAPS_IDX));
 	File::CreateFullPath(File::GetUserPath(D_SCREENSHOTS_IDX));
 	File::CreateFullPath(File::GetUserPath(D_SHADERS_IDX));
+	File::CreateFullPath(File::GetUserPath(D_SHADERS_IDX) + ANAGLYPH_DIR DIR_SEP);
 	File::CreateFullPath(File::GetUserPath(D_STATESAVES_IDX));
 	File::CreateFullPath(File::GetUserPath(D_THEMES_IDX));
 }
diff --git a/Source/Core/VideoBackends/D3D/main.cpp b/Source/Core/VideoBackends/D3D/main.cpp
index 9e8d0661ed..57e47fd629 100644
--- a/Source/Core/VideoBackends/D3D/main.cpp
+++ b/Source/Core/VideoBackends/D3D/main.cpp
@@ -81,6 +81,7 @@ void InitBackendInfo()
 	g_Config.backend_info.bSupportsOversizedViewports = false;
 	g_Config.backend_info.bSupportsGeometryShaders = true;
 	g_Config.backend_info.bSupports3DVision = true;
+	g_Config.backend_info.bSupportsPostProcessing = false;
 
 	IDXGIFactory* factory;
 	IDXGIAdapter* ad;
@@ -133,6 +134,7 @@ void InitBackendInfo()
 
 	// Clear ppshaders string vector
 	g_Config.backend_info.PPShaders.clear();
+	g_Config.backend_info.AnaglyphShaders.clear();
 
 	DX11::D3D::UnloadDXGI();
 	DX11::D3D::UnloadD3D();
diff --git a/Source/Core/VideoBackends/OGL/PostProcessing.cpp b/Source/Core/VideoBackends/OGL/PostProcessing.cpp
index 3c1bb386bf..3fa6f26de9 100644
--- a/Source/Core/VideoBackends/OGL/PostProcessing.cpp
+++ b/Source/Core/VideoBackends/OGL/PostProcessing.cpp
@@ -36,29 +36,10 @@ static const char s_vertex_shader[] =
 	"	uv0 = rawpos * src_rect.zw + src_rect.xy;\n"
 	"}\n";
 
-// Anaglyph Red-Cyan shader based on Dubois algorithm
-// Constants taken from the paper:
-// "Conversion of a Stereo Pair to Anaglyph with
-// the Least-Squares Projection Method"
-// Eric Dubois, March 2009
-static const char s_anaglyph_shader[] =
-	"void main() {\n"
-	"	vec4 c0 = SampleLayer(0);\n"
-	"	vec4 c1 = SampleLayer(1);\n"
-	"	mat3 l = mat3( 0.437, 0.449, 0.164,\n"
-	"	              -0.062,-0.062,-0.024,\n"
-	"	              -0.048,-0.050,-0.017);\n"
-	"	mat3 r = mat3(-0.011,-0.032,-0.007,\n"
-	"	               0.377, 0.761, 0.009,\n"
-	"	              -0.026,-0.093, 1.234);\n"
-	"	SetOutput(vec4(c0.rgb * l + c1.rgb * r, c0.a));\n"
-	"}\n";
-
 static const char s_default_shader[] = "void main() { SetOutput(Sample()); }\n";
 
 OpenGLPostProcessing::OpenGLPostProcessing()
 	: m_initialized(false)
-	, m_anaglyph(false)
 {
 	CreateHeader();
 
@@ -183,8 +164,7 @@ void OpenGLPostProcessing::BlitFromTexture(TargetRectangle src, TargetRectangle
 void OpenGLPostProcessing::ApplyShader()
 {
 	// shader didn't changed
-	if (m_initialized && m_config.GetShader() == g_ActiveConfig.sPostProcessingShader &&
-			((g_ActiveConfig.iStereoMode == STEREO_ANAGLYPH) == m_anaglyph))
+	if (m_initialized && m_config.GetShader() == g_ActiveConfig.sPostProcessingShader)
 		return;
 
 	m_shader.Destroy();
@@ -192,9 +172,7 @@ void OpenGLPostProcessing::ApplyShader()
 
 	// load shader code
 	std::string code = "";
-	if (g_ActiveConfig.iStereoMode == STEREO_ANAGLYPH)
-		code = s_anaglyph_shader;
-	else if (g_ActiveConfig.sPostProcessingShader != "")
+	if (g_ActiveConfig.sPostProcessingShader != "")
 		code = m_config.LoadShader();
 
 	if (code == "")
@@ -244,7 +222,6 @@ void OpenGLPostProcessing::ApplyShader()
 		std::string glsl_name = "option_" + it.first;
 		m_uniform_bindings[it.first] = glGetUniformLocation(m_shader.glprogid, glsl_name.c_str());
 	}
-	m_anaglyph = g_ActiveConfig.iStereoMode == STEREO_ANAGLYPH;
 	m_initialized = true;
 }
 
diff --git a/Source/Core/VideoBackends/OGL/PostProcessing.h b/Source/Core/VideoBackends/OGL/PostProcessing.h
index e2be0bdc7d..4c67eca839 100644
--- a/Source/Core/VideoBackends/OGL/PostProcessing.h
+++ b/Source/Core/VideoBackends/OGL/PostProcessing.h
@@ -28,7 +28,6 @@ public:
 
 private:
 	bool m_initialized;
-	bool m_anaglyph;
 	SHADER m_shader;
 	GLuint m_uniform_resolution;
 	GLuint m_uniform_src_rect;
diff --git a/Source/Core/VideoBackends/OGL/main.cpp b/Source/Core/VideoBackends/OGL/main.cpp
index f549fed5d6..68565e50fd 100644
--- a/Source/Core/VideoBackends/OGL/main.cpp
+++ b/Source/Core/VideoBackends/OGL/main.cpp
@@ -95,14 +95,14 @@ std::string VideoBackend::GetDisplayName() const
 		return "OpenGL";
 }
 
-static void GetShaders(std::vector<std::string> &shaders)
+static void GetShaders(std::vector<std::string> &shaders, const std::string &sub_dir = "")
 {
 	std::set<std::string> already_found;
 
 	shaders.clear();
-	static const std::string directories[] = {
-		File::GetUserPath(D_SHADERS_IDX),
-		File::GetSysDirectory() + SHADERS_DIR DIR_SEP,
+	const std::string directories[] = {
+		File::GetUserPath(D_SHADERS_IDX) + sub_dir,
+		File::GetSysDirectory() + SHADERS_DIR DIR_SEP + sub_dir,
 	};
 	for (auto& directory : directories)
 	{
@@ -139,6 +139,7 @@ static void InitBackendInfo()
 	g_Config.backend_info.bSupportsOversizedViewports = true;
 	g_Config.backend_info.bSupportsGeometryShaders = true;
 	g_Config.backend_info.bSupports3DVision = false;
+	g_Config.backend_info.bSupportsPostProcessing = true;
 
 	g_Config.backend_info.Adapters.clear();
 
@@ -148,6 +149,7 @@ static void InitBackendInfo()
 
 	// pp shaders
 	GetShaders(g_Config.backend_info.PPShaders);
+	GetShaders(g_Config.backend_info.AnaglyphShaders, std::string(ANAGLYPH_DIR DIR_SEP));
 }
 
 void VideoBackend::ShowConfig(void *_hParent)
diff --git a/Source/Core/VideoCommon/PostProcessing.cpp b/Source/Core/VideoCommon/PostProcessing.cpp
index b4ee1e8702..c27b0f89fc 100644
--- a/Source/Core/VideoCommon/PostProcessing.cpp
+++ b/Source/Core/VideoCommon/PostProcessing.cpp
@@ -30,14 +30,16 @@ std::string PostProcessingShaderConfiguration::LoadShader(std::string shader)
 		shader = g_ActiveConfig.sPostProcessingShader;
 	m_current_shader = shader;
 
+	const std::string sub_dir = (g_Config.iStereoMode == STEREO_ANAGLYPH) ? ANAGLYPH_DIR DIR_SEP : "";
+
 	// loading shader code
 	std::string code;
-	std::string path = File::GetUserPath(D_SHADERS_IDX) + shader + ".glsl";
+	std::string path = File::GetUserPath(D_SHADERS_IDX) + sub_dir + shader + ".glsl";
 
 	if (!File::Exists(path))
 	{
 		// Fallback to shared user dir
-		path = File::GetSysDirectory() + SHADERS_DIR DIR_SEP + shader + ".glsl";
+		path = File::GetSysDirectory() + SHADERS_DIR DIR_SEP + sub_dir + shader + ".glsl";
 	}
 
 	if (!File::ReadFileToString(path, code))
diff --git a/Source/Core/VideoCommon/VideoConfig.h b/Source/Core/VideoCommon/VideoConfig.h
index cf6ea92b32..69684557e8 100644
--- a/Source/Core/VideoCommon/VideoConfig.h
+++ b/Source/Core/VideoCommon/VideoConfig.h
@@ -147,6 +147,7 @@ struct VideoConfig final
 		std::vector<std::string> Adapters; // for D3D
 		std::vector<std::string> AAModes;
 		std::vector<std::string> PPShaders; // post-processing shaders
+		std::vector<std::string> AnaglyphShaders; // anaglyph shaders
 
 		bool bSupportsExclusiveFullscreen;
 		bool bSupportsDualSourceBlend;
@@ -158,6 +159,7 @@ struct VideoConfig final
 		bool bSupportsBindingLayout; // Needed by ShaderGen, so must stay in VideoCommon
 		bool bSupportsBBox;
 		bool bSupportsGSInstancing; // Needed by GeometryShaderGen, so must stay in VideoCommon
+		bool bSupportsPostProcessing;
 	} backend_info;
 
 	// Utility