diff --git a/Source/Core/VideoCommon/GeometryShaderGen.cpp b/Source/Core/VideoCommon/GeometryShaderGen.cpp
index 187af8b088..57009aedaa 100644
--- a/Source/Core/VideoCommon/GeometryShaderGen.cpp
+++ b/Source/Core/VideoCommon/GeometryShaderGen.cpp
@@ -53,17 +53,22 @@ static inline void GenerateGeometryShader(T& out, u32 components, API_TYPE ApiTy
 	uid_data->pixel_lighting = g_ActiveConfig.bEnablePixelLighting;
 
 	GenerateVSOutputStruct<T>(out, ApiType);
-	GenerateGSOutputStruct<T>(out, ApiType);
 
 	if (ApiType == API_OPENGL)
 	{
 		out.Write("centroid in VS_OUTPUT o[3];\n");
-		out.Write("centroid out GS_OUTPUT gs;\n");
+		out.Write("centroid out VS_OUTPUT vs;\n");
+		out.Write("flat out int layer;\n");
 
 		out.Write("void main()\n{\n");
 	}
 	else // D3D
 	{
+		out.Write("struct GS_OUTPUT {\n");
+		out.Write("\tVS_OUTPUT vs;\n");
+		out.Write("\tuint layer : SV_RenderTargetArrayIndex;\n");
+		out.Write("};\n");
+
 		if (g_ActiveConfig.backend_info.bSupportsGSInstancing)
 		{
 			out.Write("[maxvertexcount(3)]\n[instance(%d)]\n", g_ActiveConfig.iStereoMode > 0 ? 2 : 1);
@@ -85,19 +90,23 @@ static inline void GenerateGeometryShader(T& out, u32 components, API_TYPE ApiTy
 	if (g_ActiveConfig.backend_info.bSupportsGSInstancing)
 	{
 		if (ApiType == API_OPENGL)
-			out.Write("\tint layer = gl_InvocationID;\n");
+			out.Write("\tint eye = gl_InvocationID;\n");
 		else
-			out.Write("\tint layer = InstanceID;\n");
+			out.Write("\tint eye = InstanceID;\n");
 	}
 	else
-		out.Write("\tfor (int layer = 0; layer < %d; ++layer) {\n", g_ActiveConfig.iStereoMode > 0 ? 2 : 1);
+		out.Write("\tfor (int eye = 0; eye < %d; ++eye) {\n", g_ActiveConfig.iStereoMode > 0 ? 2 : 1);
 
 	out.Write("\tfor (int i = 0; i < 3; ++i) {\n");
 
 	// Select the output layer
-	out.Write("\t\tgs.layer = layer;\n");
 	if (ApiType == API_OPENGL)
-		out.Write("\t\tgl_Layer = layer;\n");
+	{
+		out.Write("\t\tgl_Layer = eye;\n");
+		out.Write("\t\tlayer = eye;\n");
+	}
+	else
+		out.Write("\t\tgs.layer = eye;\n");
 
 	out.Write("\t\tf = o[i];\n");
 	out.Write("\t\tfloat4 pos = o[i].pos;\n");
@@ -111,8 +120,8 @@ static inline void GenerateGeometryShader(T& out, u32 components, API_TYPE ApiTy
 		// the depth value. This results in objects at a distance smaller than the convergence
 		// distance to seemingly appear in front of the screen.
 		// This formula is based on page 13 of the "Nvidia 3D Vision Automatic, Best Practices Guide"
-		out.Write("\t\tf.clipPos.x = o[i].clipPos.x + " I_STEREOPARAMS"[layer] * (o[i].clipPos.w - " I_STEREOPARAMS"[2]);\n");
-		out.Write("\t\tpos.x = o[i].pos.x + " I_STEREOPARAMS"[layer] * (o[i].pos.w - " I_STEREOPARAMS"[2]);\n");
+		out.Write("\t\tf.clipPos.x = o[i].clipPos.x + " I_STEREOPARAMS"[eye] * (o[i].clipPos.w - " I_STEREOPARAMS"[2]);\n");
+		out.Write("\t\tpos.x = o[i].pos.x + " I_STEREOPARAMS"[eye] * (o[i].pos.w - " I_STEREOPARAMS"[2]);\n");
 	}
 
 	out.Write("\t\tf.pos.x = pos.x;\n");
@@ -120,7 +129,7 @@ static inline void GenerateGeometryShader(T& out, u32 components, API_TYPE ApiTy
 	if (ApiType == API_OPENGL)
 		out.Write("\t\tgl_Position = pos;\n");
 
-	out.Write("\t\tgs.vs = f;\n");
+	out.Write("\t\t%s = f;\n", (ApiType == API_OPENGL) ? "vs" : "gs.vs");
 
 	if (ApiType == API_OPENGL)
 		out.Write("\t\tEmitVertex();\n");
diff --git a/Source/Core/VideoCommon/PixelShaderGen.cpp b/Source/Core/VideoCommon/PixelShaderGen.cpp
index b925b826d3..48cd5b8fec 100644
--- a/Source/Core/VideoCommon/PixelShaderGen.cpp
+++ b/Source/Core/VideoCommon/PixelShaderGen.cpp
@@ -265,7 +265,6 @@ static inline void GeneratePixelShader(T& out, DSTALPHA_MODE dstAlphaMode, API_T
 	}
 
 	GenerateVSOutputStruct<T>(out, ApiType);
-	GenerateGSOutputStruct<T>(out, ApiType);
 
 	const bool forced_early_z = g_ActiveConfig.backend_info.bSupportsEarlyZ && bpmem.UseEarlyDepthTest() && (g_ActiveConfig.bFastDepthCalc || bpmem.alpha_test.TestResult() == AlphaTest::UNDETERMINED);
 	const bool per_pixel_depth = (bpmem.ztex2.op != ZTEXTURE_DISABLE && bpmem.UseLateDepthTest()) || (!g_ActiveConfig.bFastDepthCalc && bpmem.zmode.testenable && !forced_early_z);
@@ -320,7 +319,8 @@ static inline void GeneratePixelShader(T& out, DSTALPHA_MODE dstAlphaMode, API_T
 		uid_data->stereo = g_ActiveConfig.iStereoMode > 0;
 		if (g_ActiveConfig.iStereoMode > 0)
 		{
-			out.Write("centroid in GS_OUTPUT gs;\n");
+			out.Write("centroid in VS_OUTPUT vs;\n");
+			out.Write("flat in int layer;\n");
 		}
 		else
 		{
@@ -348,19 +348,19 @@ static inline void GeneratePixelShader(T& out, DSTALPHA_MODE dstAlphaMode, API_T
 			// Let's set up attributes
 			for (unsigned int i = 0; i < numTexgen; ++i)
 			{
-				out.Write("\tfloat3 uv%d = gs.vs.tex%d;\n", i, i);
+				out.Write("\tfloat3 uv%d = vs.tex%d;\n", i, i);
 			}
-			out.Write("\tfloat4 clipPos = gs.vs.clipPos;\n");
+			out.Write("\tfloat4 clipPos = vs.clipPos;\n");
 			if (g_ActiveConfig.bEnablePixelLighting)
 			{
-				out.Write("\tfloat4 Normal = gs.vs.Normal;\n");
+				out.Write("\tfloat4 Normal = vs.Normal;\n");
 			}
 		}
 
 		// On Mali, global variables must be initialized as constants.
 		// This is why we initialize these variables locally instead.
-		out.Write("\tfloat4 colors_0 = %s;\n", (g_ActiveConfig.iStereoMode > 0) ? "gs.vs.colors_0" : "colors_02");
-		out.Write("\tfloat4 colors_1 = %s;\n", (g_ActiveConfig.iStereoMode > 0) ? "gs.vs.colors_1" : "colors_12");
+		out.Write("\tfloat4 colors_0 = %s;\n", (g_ActiveConfig.iStereoMode > 0) ? "vs.colors_0" : "colors_02");
+		out.Write("\tfloat4 colors_1 = %s;\n", (g_ActiveConfig.iStereoMode > 0) ? "vs.colors_1" : "colors_12");
 
 		out.Write("\tfloat4 rawpos = gl_FragCoord;\n");
 	}
@@ -943,7 +943,7 @@ static inline void SampleTexture(T& out, const char *texcoords, const char *texs
 	if (ApiType == API_D3D)
 		out.Write("iround(255.0 * Tex%d.Sample(samp%d, float3(%s.xy * " I_TEXDIMS"[%d].xy, %s))).%s;\n", texmap, texmap, texcoords, texmap, g_ActiveConfig.iStereoMode > 0 ? "layer" : "0.0", texswap);
 	else
-		out.Write("iround(255.0 * texture(samp%d, float3(%s.xy * " I_TEXDIMS"[%d].xy, %s))).%s;\n", texmap, texcoords, texmap, g_ActiveConfig.iStereoMode > 0 ? "gs.layer" : "0.0", texswap);
+		out.Write("iround(255.0 * texture(samp%d, float3(%s.xy * " I_TEXDIMS"[%d].xy, %s))).%s;\n", texmap, texcoords, texmap, g_ActiveConfig.iStereoMode > 0 ? "layer" : "0.0", texswap);
 }
 
 static const char *tevAlphaFuncsTable[] =
diff --git a/Source/Core/VideoCommon/ShaderGenCommon.h b/Source/Core/VideoCommon/ShaderGenCommon.h
index ed9bab9fca..618d262374 100644
--- a/Source/Core/VideoCommon/ShaderGenCommon.h
+++ b/Source/Core/VideoCommon/ShaderGenCommon.h
@@ -258,17 +258,6 @@ static inline void GenerateVSOutputStruct(T& object, API_TYPE api_type)
 	object.Write("};\n");
 }
 
-template<class T>
-static inline void GenerateGSOutputStruct(T& object, API_TYPE api_type)
-{
-	object.Write("struct GS_OUTPUT {\n");
-
-	DefineOutputStructMember(object, api_type, "VS_OUTPUT", "vs", -1, "");
-	DefineOutputStructMember(object, api_type, (api_type == API_OPENGL) ? "flat int" : "uint", "layer", -1, "SV_RenderTargetArrayIndex");
-
-	object.Write("};\n");
-}
-
 // Constant variable names
 #define I_COLORS        "color"
 #define I_KCOLORS       "k"