diff --git a/Data/User/Shaders/16bit.txt b/Data/Sys/Shaders/16bit.glsl
similarity index 100%
rename from Data/User/Shaders/16bit.txt
rename to Data/Sys/Shaders/16bit.glsl
diff --git a/Data/User/Shaders/32bit.txt b/Data/Sys/Shaders/32bit.glsl
similarity index 100%
rename from Data/User/Shaders/32bit.txt
rename to Data/Sys/Shaders/32bit.glsl
diff --git a/Data/User/Shaders/README.txt b/Data/Sys/Shaders/README.txt
similarity index 100%
rename from Data/User/Shaders/README.txt
rename to Data/Sys/Shaders/README.txt
diff --git a/Data/User/Shaders/acidmetal.txt b/Data/Sys/Shaders/acidmetal.glsl
similarity index 100%
rename from Data/User/Shaders/acidmetal.txt
rename to Data/Sys/Shaders/acidmetal.glsl
diff --git a/Data/User/Shaders/acidtrip.txt b/Data/Sys/Shaders/acidtrip.glsl
similarity index 100%
rename from Data/User/Shaders/acidtrip.txt
rename to Data/Sys/Shaders/acidtrip.glsl
diff --git a/Data/User/Shaders/acidtrip2.txt b/Data/Sys/Shaders/acidtrip2.glsl
similarity index 100%
rename from Data/User/Shaders/acidtrip2.txt
rename to Data/Sys/Shaders/acidtrip2.glsl
diff --git a/Data/User/Shaders/asciiart.txt b/Data/Sys/Shaders/asciiart.glsl
similarity index 100%
rename from Data/User/Shaders/asciiart.txt
rename to Data/Sys/Shaders/asciiart.glsl
diff --git a/Data/User/Shaders/auto_toon.txt b/Data/Sys/Shaders/auto_toon.glsl
similarity index 100%
rename from Data/User/Shaders/auto_toon.txt
rename to Data/Sys/Shaders/auto_toon.glsl
diff --git a/Data/User/Shaders/auto_toon2.txt b/Data/Sys/Shaders/auto_toon2.glsl
similarity index 100%
rename from Data/User/Shaders/auto_toon2.txt
rename to Data/Sys/Shaders/auto_toon2.glsl
diff --git a/Data/User/Shaders/bad_bloom.txt b/Data/Sys/Shaders/bad_bloom.glsl
similarity index 100%
rename from Data/User/Shaders/bad_bloom.txt
rename to Data/Sys/Shaders/bad_bloom.glsl
diff --git a/Data/User/Shaders/brighten.txt b/Data/Sys/Shaders/brighten.glsl
similarity index 100%
rename from Data/User/Shaders/brighten.txt
rename to Data/Sys/Shaders/brighten.glsl
diff --git a/Data/User/Shaders/chrismas.txt b/Data/Sys/Shaders/chrismas.glsl
similarity index 100%
rename from Data/User/Shaders/chrismas.txt
rename to Data/Sys/Shaders/chrismas.glsl
diff --git a/Data/User/Shaders/cool1.txt b/Data/Sys/Shaders/cool1.glsl
similarity index 100%
rename from Data/User/Shaders/cool1.txt
rename to Data/Sys/Shaders/cool1.glsl
diff --git a/Data/User/Shaders/darkerbrighter.txt b/Data/Sys/Shaders/darkerbrighter.glsl
similarity index 100%
rename from Data/User/Shaders/darkerbrighter.txt
rename to Data/Sys/Shaders/darkerbrighter.glsl
diff --git a/Data/User/Shaders/emboss.txt b/Data/Sys/Shaders/emboss.glsl
similarity index 100%
rename from Data/User/Shaders/emboss.txt
rename to Data/Sys/Shaders/emboss.glsl
diff --git a/Data/User/Shaders/fire.txt b/Data/Sys/Shaders/fire.glsl
similarity index 100%
rename from Data/User/Shaders/fire.txt
rename to Data/Sys/Shaders/fire.glsl
diff --git a/Data/User/Shaders/fire2.txt b/Data/Sys/Shaders/fire2.glsl
similarity index 100%
rename from Data/User/Shaders/fire2.txt
rename to Data/Sys/Shaders/fire2.glsl
diff --git a/Data/User/Shaders/firewater.txt b/Data/Sys/Shaders/firewater.glsl
similarity index 100%
rename from Data/User/Shaders/firewater.txt
rename to Data/Sys/Shaders/firewater.glsl
diff --git a/Data/User/Shaders/grayscale.txt b/Data/Sys/Shaders/grayscale.glsl
similarity index 100%
rename from Data/User/Shaders/grayscale.txt
rename to Data/Sys/Shaders/grayscale.glsl
diff --git a/Data/User/Shaders/grayscale2.txt b/Data/Sys/Shaders/grayscale2.glsl
similarity index 100%
rename from Data/User/Shaders/grayscale2.txt
rename to Data/Sys/Shaders/grayscale2.glsl
diff --git a/Data/User/Shaders/invert.txt b/Data/Sys/Shaders/invert.glsl
similarity index 100%
rename from Data/User/Shaders/invert.txt
rename to Data/Sys/Shaders/invert.glsl
diff --git a/Data/User/Shaders/invert_blue.txt b/Data/Sys/Shaders/invert_blue.glsl
similarity index 100%
rename from Data/User/Shaders/invert_blue.txt
rename to Data/Sys/Shaders/invert_blue.glsl
diff --git a/Data/User/Shaders/invertedoutline.txt b/Data/Sys/Shaders/invertedoutline.glsl
similarity index 100%
rename from Data/User/Shaders/invertedoutline.txt
rename to Data/Sys/Shaders/invertedoutline.glsl
diff --git a/Data/User/Shaders/mad_world.txt b/Data/Sys/Shaders/mad_world.glsl
similarity index 100%
rename from Data/User/Shaders/mad_world.txt
rename to Data/Sys/Shaders/mad_world.glsl
diff --git a/Data/User/Shaders/nightvision.txt b/Data/Sys/Shaders/nightvision.glsl
similarity index 100%
rename from Data/User/Shaders/nightvision.txt
rename to Data/Sys/Shaders/nightvision.glsl
diff --git a/Data/User/Shaders/nightvision2.txt b/Data/Sys/Shaders/nightvision2.glsl
similarity index 100%
rename from Data/User/Shaders/nightvision2.txt
rename to Data/Sys/Shaders/nightvision2.glsl
diff --git a/Data/User/Shaders/nightvision2scanlines.txt b/Data/Sys/Shaders/nightvision2scanlines.glsl
similarity index 100%
rename from Data/User/Shaders/nightvision2scanlines.txt
rename to Data/Sys/Shaders/nightvision2scanlines.glsl
diff --git a/Data/User/Shaders/posterize.txt b/Data/Sys/Shaders/posterize.glsl
similarity index 100%
rename from Data/User/Shaders/posterize.txt
rename to Data/Sys/Shaders/posterize.glsl
diff --git a/Data/User/Shaders/posterize2.txt b/Data/Sys/Shaders/posterize2.glsl
similarity index 100%
rename from Data/User/Shaders/posterize2.txt
rename to Data/Sys/Shaders/posterize2.glsl
diff --git a/Data/User/Shaders/primarycolors.txt b/Data/Sys/Shaders/primarycolors.glsl
similarity index 100%
rename from Data/User/Shaders/primarycolors.txt
rename to Data/Sys/Shaders/primarycolors.glsl
diff --git a/Data/User/Shaders/sepia.txt b/Data/Sys/Shaders/sepia.glsl
similarity index 100%
rename from Data/User/Shaders/sepia.txt
rename to Data/Sys/Shaders/sepia.glsl
diff --git a/Data/User/Shaders/sketchy.txt b/Data/Sys/Shaders/sketchy.glsl
similarity index 100%
rename from Data/User/Shaders/sketchy.txt
rename to Data/Sys/Shaders/sketchy.glsl
diff --git a/Data/User/Shaders/spookey1.txt b/Data/Sys/Shaders/spookey1.glsl
similarity index 100%
rename from Data/User/Shaders/spookey1.txt
rename to Data/Sys/Shaders/spookey1.glsl
diff --git a/Data/User/Shaders/spookey2.txt b/Data/Sys/Shaders/spookey2.glsl
similarity index 100%
rename from Data/User/Shaders/spookey2.txt
rename to Data/Sys/Shaders/spookey2.glsl
diff --git a/Data/User/Shaders/stereoscopic.txt b/Data/Sys/Shaders/stereoscopic.glsl
similarity index 100%
rename from Data/User/Shaders/stereoscopic.txt
rename to Data/Sys/Shaders/stereoscopic.glsl
diff --git a/Data/User/Shaders/stereoscopic2.txt b/Data/Sys/Shaders/stereoscopic2.glsl
similarity index 100%
rename from Data/User/Shaders/stereoscopic2.txt
rename to Data/Sys/Shaders/stereoscopic2.glsl
diff --git a/Data/User/Shaders/sunset.txt b/Data/Sys/Shaders/sunset.glsl
similarity index 100%
rename from Data/User/Shaders/sunset.txt
rename to Data/Sys/Shaders/sunset.glsl
diff --git a/Data/User/Shaders/swap_RGB_BGR.txt b/Data/Sys/Shaders/swap_RGB_BGR.glsl
similarity index 100%
rename from Data/User/Shaders/swap_RGB_BGR.txt
rename to Data/Sys/Shaders/swap_RGB_BGR.glsl
diff --git a/Data/User/Shaders/swap_RGB_BRG.txt b/Data/Sys/Shaders/swap_RGB_BRG.glsl
similarity index 100%
rename from Data/User/Shaders/swap_RGB_BRG.txt
rename to Data/Sys/Shaders/swap_RGB_BRG.glsl
diff --git a/Data/User/Shaders/swap_RGB_GBR.txt b/Data/Sys/Shaders/swap_RGB_GBR.glsl
similarity index 100%
rename from Data/User/Shaders/swap_RGB_GBR.txt
rename to Data/Sys/Shaders/swap_RGB_GBR.glsl
diff --git a/Data/User/Shaders/swap_RGB_GRB.txt b/Data/Sys/Shaders/swap_RGB_GRB.glsl
similarity index 100%
rename from Data/User/Shaders/swap_RGB_GRB.txt
rename to Data/Sys/Shaders/swap_RGB_GRB.glsl
diff --git a/Data/User/Shaders/swap_RGB_RBG.txt b/Data/Sys/Shaders/swap_RGB_RBG.glsl
similarity index 100%
rename from Data/User/Shaders/swap_RGB_RBG.txt
rename to Data/Sys/Shaders/swap_RGB_RBG.glsl
diff --git a/Data/User/Shaders/toxic.txt b/Data/Sys/Shaders/toxic.glsl
similarity index 100%
rename from Data/User/Shaders/toxic.txt
rename to Data/Sys/Shaders/toxic.glsl
diff --git a/Source/Core/DolphinWX/Src/Main.cpp b/Source/Core/DolphinWX/Src/Main.cpp
index 9fae1f2999..7ba77501c0 100644
--- a/Source/Core/DolphinWX/Src/Main.cpp
+++ b/Source/Core/DolphinWX/Src/Main.cpp
@@ -253,27 +253,26 @@ bool DolphinApp::OnInit()
 	//TODO : detect the revision and upgrade where necessary
 	File::CopyDir(std::string(SHARED_USER_DIR GAMECONFIG_DIR DIR_SEP),
 			File::GetUserPath(D_GAMECONFIG_IDX));
-	File::CopyDir(std::string(SHARED_USER_DIR SHADERS_DIR DIR_SEP),
-			File::GetUserPath(D_SHADERS_IDX));
 	File::CopyDir(std::string(SHARED_USER_DIR WII_USER_DIR DIR_SEP),
 			File::GetUserPath(D_WIIUSER_IDX));
 	File::CopyDir(std::string(SHARED_USER_DIR OPENCL_DIR DIR_SEP),
 			File::GetUserPath(D_OPENCL_IDX));
 
 	File::CreateFullPath(File::GetUserPath(D_USER_IDX));
-	File::CreateFullPath(File::GetUserPath(D_CONFIG_IDX));
-	File::CreateFullPath(File::GetUserPath(D_GCUSER_IDX));
 	File::CreateFullPath(File::GetUserPath(D_CACHE_IDX));
+	File::CreateFullPath(File::GetUserPath(D_CONFIG_IDX));
 	File::CreateFullPath(File::GetUserPath(D_DUMPDSP_IDX));
 	File::CreateFullPath(File::GetUserPath(D_DUMPTEXTURES_IDX));
-	File::CreateFullPath(File::GetUserPath(D_HIRESTEXTURES_IDX));
-	File::CreateFullPath(File::GetUserPath(D_SCREENSHOTS_IDX));
-	File::CreateFullPath(File::GetUserPath(D_STATESAVES_IDX));
-	File::CreateFullPath(File::GetUserPath(D_MAILLOGS_IDX));
-	File::CreateFullPath(File::GetUserPath(D_MAPS_IDX));
+	File::CreateFullPath(File::GetUserPath(D_GCUSER_IDX));
 	File::CreateFullPath(File::GetUserPath(D_GCUSER_IDX) + USA_DIR DIR_SEP);
 	File::CreateFullPath(File::GetUserPath(D_GCUSER_IDX) + EUR_DIR DIR_SEP);
 	File::CreateFullPath(File::GetUserPath(D_GCUSER_IDX) + JAP_DIR DIR_SEP);
+	File::CreateFullPath(File::GetUserPath(D_HIRESTEXTURES_IDX));
+	File::CreateFullPath(File::GetUserPath(D_MAILLOGS_IDX));
+	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_STATESAVES_IDX));
 
 	LogManager::Init();
 	SConfig::Init();
diff --git a/Source/Plugins/Plugin_VideoOGL/Src/PostProcessing.cpp b/Source/Plugins/Plugin_VideoOGL/Src/PostProcessing.cpp
index d5899038fc..c1563a74e2 100644
--- a/Source/Plugins/Plugin_VideoOGL/Src/PostProcessing.cpp
+++ b/Source/Plugins/Plugin_VideoOGL/Src/PostProcessing.cpp
@@ -2,6 +2,7 @@
 // Licensed under GPLv2
 // Refer to the license.txt file included.
 
+#include "CommonPaths.h"
 #include "FileUtil.h"
 #include "VideoCommon.h"
 #include "VideoConfig.h"
@@ -150,7 +151,12 @@ void ApplyShader()
 	
 	// loading shader code
 	std::string code;
-	std::string path = File::GetUserPath(D_SHADERS_IDX) + g_ActiveConfig.sPostProcessingShader + ".txt";
+	std::string path = File::GetUserPath(D_SHADERS_IDX) + g_ActiveConfig.sPostProcessingShader + ".glsl";
+	if (!File::Exists(path))
+	{
+		// Fallback to shared user dir
+		path = File::GetSysDirectory() + SHADERS_DIR DIR_SEP + g_ActiveConfig.sPostProcessingShader + ".glsl";
+	}
 	if(!File::ReadFileToString(true, path.c_str(), code)) {
 		ERROR_LOG(VIDEO, "Post-processing shader not found: %s", path.c_str());
 		return;
diff --git a/Source/Plugins/Plugin_VideoOGL/Src/main.cpp b/Source/Plugins/Plugin_VideoOGL/Src/main.cpp
index 1eb986fe74..9e38b80fed 100644
--- a/Source/Plugins/Plugin_VideoOGL/Src/main.cpp
+++ b/Source/Plugins/Plugin_VideoOGL/Src/main.cpp
@@ -38,6 +38,7 @@ Make AA apply instantly during gameplay if possible
 
 #include "Globals.h"
 #include "Atomic.h"
+#include "CommonPaths.h"
 #include "Thread.h"
 #include "LogManager.h"
 
@@ -102,25 +103,37 @@ std::string VideoBackend::GetDisplayName()
 
 void GetShaders(std::vector<std::string> &shaders)
 {
+	std::set<std::string> already_found;
+
 	shaders.clear();
-	if (File::IsDirectory(File::GetUserPath(D_SHADERS_IDX)))
+	static const std::string directories[] = {
+		File::GetUserPath(D_SHADERS_IDX),
+		File::GetSysDirectory() + SHADERS_DIR DIR_SEP,
+	};
+	for (size_t i = 0; i < ArraySize(directories); ++i)
 	{
+		if (!File::IsDirectory(directories[i]))
+			continue;
+
 		File::FSTEntry entry;
-		File::ScanDirectoryTree(File::GetUserPath(D_SHADERS_IDX), entry);
-		for (u32 i = 0; i < entry.children.size(); i++) 
+		File::ScanDirectoryTree(directories[i], entry);
+		for (u32 j = 0; j < entry.children.size(); j++)
 		{
-			std::string name = entry.children[i].virtualName.c_str();
-			if (!strcasecmp(name.substr(name.size() - 4).c_str(), ".txt")) {
-				name = name.substr(0, name.size() - 4);
-				shaders.push_back(name);
-			}
+			std::string name = entry.children[j].virtualName.c_str();
+			if (name.size() < 5)
+				continue;
+			if (strcasecmp(name.substr(name.size() - 5).c_str(), ".glsl"))
+				continue;
+
+			name = name.substr(0, name.size() - 5);
+			if (already_found.find(name) != already_found.end())
+				continue;
+
+			already_found.insert(name);
+			shaders.push_back(name);
 		}
-		std::sort(shaders.begin(), shaders.end());
-	}
-	else
-	{
-		File::CreateDir(File::GetUserPath(D_SHADERS_IDX).c_str());
 	}
+	std::sort(shaders.begin(), shaders.end());
 }
 
 void InitBackendInfo()