diff --git a/Source/cmCommandArgumentParserHelper.cxx b/Source/cmCommandArgumentParserHelper.cxx
index 1460e5ddd..e9381d4c6 100644
--- a/Source/cmCommandArgumentParserHelper.cxx
+++ b/Source/cmCommandArgumentParserHelper.cxx
@@ -21,6 +21,7 @@ int cmCommandArgument_yyparse( yyscan_t yyscanner );
 cmCommandArgumentParserHelper::cmCommandArgumentParserHelper()
 {
   this->WarnUninitialized = false;
+  this->CheckSystemVars = false;
   this->FileLine = -1;
   this->FileName = 0;
   this->RemoveEmpty = true;
@@ -129,10 +130,14 @@ char* cmCommandArgumentParserHelper::ExpandVariable(const char* var)
     // not been "cleared"/initialized with a set(foo ) call
     if(this->WarnUninitialized && !this->Makefile->VariableInitialized(var))
       {
-      cmOStringStream msg;
-      msg << this->FileName << ":" << this->FileLine << ":" <<
-        " warning: uninitialized variable \'" << var << "\'";
-      cmSystemTools::Message(msg.str().c_str());
+      const char* root = this->Makefile->GetDefinition("CMAKE_ROOT");
+      if (this->CheckSystemVars || strstr(this->FileName, root) != this->FileName)
+        {
+        cmOStringStream msg;
+        msg << this->FileName << ":" << this->FileLine << ":" <<
+          " warning: uninitialized variable \'" << var << "\'";
+        cmSystemTools::Message(msg.str().c_str());
+        }
       }
     return 0;
     }
@@ -331,6 +336,7 @@ void cmCommandArgumentParserHelper::SetMakefile(const cmMakefile* mf)
 {
   this->Makefile = mf;
   this->WarnUninitialized = mf->GetCMakeInstance()->GetWarnUninitialized();
+  this->CheckSystemVars = mf->GetCMakeInstance()->GetCheckSystemVars();
 }
 
 void cmCommandArgumentParserHelper::SetResult(const char* value)
diff --git a/Source/cmCommandArgumentParserHelper.h b/Source/cmCommandArgumentParserHelper.h
index 1df004244..a211e952b 100644
--- a/Source/cmCommandArgumentParserHelper.h
+++ b/Source/cmCommandArgumentParserHelper.h
@@ -97,6 +97,7 @@ private:
   std::string Result;
   const char* FileName;
   bool WarnUninitialized;
+  bool CheckSystemVars;
   long FileLine;
   bool EscapeQuotes;
   std::string ErrorString;
diff --git a/Source/cmMakefile.cxx b/Source/cmMakefile.cxx
index 242900ec0..3a235905b 100644
--- a/Source/cmMakefile.cxx
+++ b/Source/cmMakefile.cxx
@@ -93,6 +93,7 @@ cmMakefile::cmMakefile(): Internal(new Internals)
   this->Initialize();
   this->PreOrder = false;
   this->WarnUnused = false;
+  this->CheckSystemVars = false;
 }
 
 cmMakefile::cmMakefile(const cmMakefile& mf): Internal(new Internals)
@@ -136,6 +137,7 @@ cmMakefile::cmMakefile(const cmMakefile& mf): Internal(new Internals)
   this->Properties = mf.Properties;
   this->PreOrder = mf.PreOrder;
   this->WarnUnused = mf.WarnUnused;
+  this->CheckSystemVars = mf.CheckSystemVars;
   this->ListFileStack = mf.ListFileStack;
   this->Initialize();
 }
@@ -774,6 +776,7 @@ void cmMakefile::SetLocalGenerator(cmLocalGenerator* lg)
       this->Internal->VarUsageStack.push(std::set<cmStdString>());
       }
     }
+    this->CheckSystemVars = this->GetCMakeInstance()->GetCheckSystemVars();
 }
 
 bool cmMakefile::NeedBackwardsCompatibility(unsigned int major,
@@ -3386,9 +3389,14 @@ void cmMakefile::PopScope()
     init.erase(*it);
     if (this->WarnUnused && usage.find(*it) == usage.end())
       {
-      cmOStringStream m;
-      m << "unused variable \'" << *it << "\'";
-      this->IssueMessage(cmake::AUTHOR_WARNING, m.str());
+      const char* cdir = this->ListFileStack.back().c_str();
+      const char* root = this->GetDefinition("CMAKE_ROOT");
+      if (this->CheckSystemVars || strstr(cdir, root) != cdir)
+        {
+        cmOStringStream m;
+        m << "unused variable \'" << *it << "\'";
+        this->IssueMessage(cmake::AUTHOR_WARNING, m.str());
+        }
       }
     else
       {
diff --git a/Source/cmMakefile.h b/Source/cmMakefile.h
index 4ce3b9b67..f1ad54d3f 100644
--- a/Source/cmMakefile.h
+++ b/Source/cmMakefile.h
@@ -935,6 +935,7 @@ private:
 
   // Unused variable flags
   bool WarnUnused;
+  bool CheckSystemVars;
 
   // stack of list files being read 
   std::deque<cmStdString> ListFileStack;
diff --git a/Source/cmake.cxx b/Source/cmake.cxx
index 93ca9e3cb..27bfbeedb 100644
--- a/Source/cmake.cxx
+++ b/Source/cmake.cxx
@@ -150,6 +150,7 @@ cmake::cmake()
   this->WarnUninitialized = false;
   this->WarnUnused = false;
   this->WarnUnusedCli = true;
+  this->CheckSystemVars = false;
   this->SuppressDevWarnings = false;
   this->DoSuppressDevWarnings = false;
   this->DebugOutput = false;
@@ -656,6 +657,11 @@ void cmake::SetArgs(const std::vector<std::string>& args)
       std::cout << "Finding unused variables given on the command line.\n";
       this->SetWarnUnusedCli(true);
       }
+    else if(arg.find("--check-system-vars",0) == 0)
+      {
+      std::cout << "Also check system files when warning about unused and uninitialized variables.\n";
+      this->SetCheckSystemVars(true);
+      }
     else if(arg.find("-G",0) == 0)
       {
       std::string value = arg.substr(2);
diff --git a/Source/cmake.h b/Source/cmake.h
index 7f7546a12..403809fcd 100644
--- a/Source/cmake.h
+++ b/Source/cmake.h
@@ -312,6 +312,8 @@ class cmake
   void SetWarnUnused(bool b) {  this->WarnUnused = b;}
   bool GetWarnUnusedCli() { return this->WarnUnusedCli;}
   void SetWarnUnusedCli(bool b) {  this->WarnUnusedCli = b;}
+  bool GetCheckSystemVars() { return this->CheckSystemVars;}
+  void SetCheckSystemVars(bool b) {  this->CheckSystemVars = b;}
 
   void MarkCliAsUsed(const std::string& variable);
 
@@ -455,6 +457,7 @@ private:
   bool WarnUninitialized;
   bool WarnUnused;
   bool WarnUnusedCli;
+  bool CheckSystemVars;
   std::map<std::string, bool> UsedCliVariables;
   std::string CMakeEditCommand;
   std::string CMakeCommand;