diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java
index f6f415e85..04a7051a7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java
@@ -89,8 +89,8 @@ public String getProperty(String key) {
 		}
 
 		public FileBasedConfig openSystemConfig(Config parent, FS fs) {
-			File prefix = fs.gitPrefix();
-			if (prefix == null) {
+			File configFile = fs.discoverGitSystemConfig();
+			if (configFile == null) {
 				return new FileBasedConfig(null, fs) {
 					public void load() {
 						// empty, do not load
@@ -102,9 +102,7 @@ public boolean isOutdated() {
 					}
 				};
 			}
-			File etc = fs.resolve(prefix, "etc"); //$NON-NLS-1$
-			File config = fs.resolve(etc, "gitconfig"); //$NON-NLS-1$
-			return new FileBasedConfig(parent, config, fs);
+			return new FileBasedConfig(parent, configFile, fs);
 		}
 
 		public FileBasedConfig openUserConfig(Config parent, FS fs) {