diff --git a/qmake/generators/makefiledeps.cpp b/qmake/generators/makefiledeps.cpp
index e1fb42e0a44..edc9a0ed7fb 100644
--- a/qmake/generators/makefiledeps.cpp
+++ b/qmake/generators/makefiledeps.cpp
@@ -679,7 +679,7 @@ bool QMakeSourceFileInfo::findDeps(SourceFile *file)
                 } else {
                     exists = QFile::exists(lfn.real());
                 }
-                if(!lfn.isNull()) {
+                if (!lfn.isNull() && !isSystemInclude(lfn.real())) {
                     dep = files->lookupFile(lfn);
                     if(!dep) {
                         dep = new SourceFile;
diff --git a/qmake/generators/unix/unixmake2.cpp b/qmake/generators/unix/unixmake2.cpp
index 8e18f69c03c..eb68614fe6c 100644
--- a/qmake/generators/unix/unixmake2.cpp
+++ b/qmake/generators/unix/unixmake2.cpp
@@ -1229,8 +1229,10 @@ void UnixMakefileGenerator::init2()
     }
 
     if (include_deps && project->isActiveConfig("gcc_MD_depends")) {
-        project->values("QMAKE_CFLAGS") += "-MD";
-        project->values("QMAKE_CXXFLAGS") += "-MD";
+        // use -MMD if we know about -isystem too
+        ProString MD_flag(project->values("QMAKE_CFLAGS_ISYSTEM").isEmpty() ? "-MD" : "-MMD");
+        project->values("QMAKE_CFLAGS") += MD_flag;
+        project->values("QMAKE_CXXFLAGS") += MD_flag;
     }
 
     if(!project->isEmpty("QMAKE_BUNDLE")) {