diff --git a/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/Indexer.kt b/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/Indexer.kt
index b35f454b51b..79f40da6140 100644
--- a/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/Indexer.kt
+++ b/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/Indexer.kt
@@ -19,7 +19,7 @@ private class EnumDefImpl(spelling: String, type: PrimitiveType) : EnumDef(spell
     override val constants = mutableListOf<EnumConstant>()
 }
 
-internal class NativeIndexImpl(val language: Language) : NativeIndex() {
+internal class NativeIndexImpl(val library: NativeLibrary) : NativeIndex() {
 
     private data class DeclarationID(val usr: String)
 
@@ -275,6 +275,11 @@ internal class NativeIndexImpl(val language: Language) : NativeIndex() {
         val entityInfo = info.entityInfo.pointed!!
         val entityName = entityInfo.name.value?.toKString()
         val kind = entityInfo.kind.value
+
+        if (!this.library.includesDeclaration(cursor)) {
+            return
+        }
+
         when (kind) {
             CXIdxEntity_Struct, CXIdxEntity_Union -> {
                 getStructDeclAt(cursor)
@@ -291,7 +296,7 @@ internal class NativeIndexImpl(val language: Language) : NativeIndex() {
                     Parameter(argName, type)
                 }
 
-                val binaryName = when (language) {
+                val binaryName = when (library.language) {
                     Language.C -> clang_Cursor_getMangling(cursor).convertAndDispose()
                 }
 
@@ -312,7 +317,7 @@ internal class NativeIndexImpl(val language: Language) : NativeIndex() {
 }
 
 fun buildNativeIndexImpl(library: NativeLibrary): NativeIndex {
-    val result = NativeIndexImpl(library.language)
+    val result = NativeIndexImpl(library)
     indexDeclarations(library, result)
     findMacroConstants(library, result)
     return result
diff --git a/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/MacroConstants.kt b/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/MacroConstants.kt
index 9ebc889aad9..7eaf2084828 100644
--- a/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/MacroConstants.kt
+++ b/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/MacroConstants.kt
@@ -201,7 +201,10 @@ private fun collectMacroConstantsNames(library: NativeLibrary): List<String> {
         val translationUnit = library.parse(index, options).ensureNoCompileErrors()
         try {
             visitChildren(translationUnit) { cursor, parent ->
-                if (cursor.kind == CXCursorKind.CXCursor_MacroDefinition && canMacroBeConstant(cursor)) {
+                if (cursor.kind == CXCursorKind.CXCursor_MacroDefinition &&
+                        library.includesDeclaration(cursor) &&
+                        canMacroBeConstant(cursor))
+                {
                     val spelling = getCursorSpelling(cursor)
                     result.add(spelling)
                 }
diff --git a/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/NativeIndex.kt b/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/NativeIndex.kt
index ac043c26072..a95916cb4d9 100644
--- a/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/NativeIndex.kt
+++ b/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/NativeIndex.kt
@@ -4,7 +4,10 @@ enum class Language {
     C
 }
 
-class NativeLibrary(val includes: List<String>, val compilerArgs: List<String>, val language: Language)
+data class NativeLibrary(val includes: List<String>,
+                         val compilerArgs: List<String>,
+                         val language: Language,
+                         val excludeSystemLibs: Boolean = true)
 
 /**
  * Retrieves the definitions from given C header file using given compiler arguments (e.g. defines).
diff --git a/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/Utils.kt b/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/Utils.kt
index 3aa8a198552..b6ed261731a 100644
--- a/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/Utils.kt
+++ b/Interop/Indexer/src/main/kotlin/org/jetbrains/kotlin/native/interop/indexer/Utils.kt
@@ -173,9 +173,16 @@ internal fun NativeLibrary.precompileHeaders(): NativeLibrary {
         clang_disposeIndex(index)
     }
 
-    return NativeLibrary(
+    return this.copy(
             includes = emptyList(),
-            compilerArgs = this.compilerArgs + listOf("-include-pch", precompiledHeader.absolutePath),
-            language = this.language
+            compilerArgs = this.compilerArgs + listOf("-include-pch", precompiledHeader.absolutePath)
     )
+}
+
+internal fun NativeLibrary.includesDeclaration(cursor: CValue<CXCursor>): Boolean {
+    return if (this.excludeSystemLibs) {
+        clang_Location_isInSystemHeader(clang_getCursorLocation(cursor)) == 0
+    } else {
+        true
+    }
 }
\ No newline at end of file
diff --git a/Interop/StubGenerator/src/main/kotlin/org/jetbrains/kotlin/native/interop/gen/jvm/main.kt b/Interop/StubGenerator/src/main/kotlin/org/jetbrains/kotlin/native/interop/gen/jvm/main.kt
index 19ac77d7ac5..91b01b6e268 100644
--- a/Interop/StubGenerator/src/main/kotlin/org/jetbrains/kotlin/native/interop/gen/jvm/main.kt
+++ b/Interop/StubGenerator/src/main/kotlin/org/jetbrains/kotlin/native/interop/gen/jvm/main.kt
@@ -266,6 +266,8 @@ private fun processLib(konanHome: String,
         defaultOpts + additionalCompilerOpts 
     val compiler = "clang"
     val language = Language.C
+    val excludeSystemLibs = config.getProperty("excludeSystemLibs")?.toBoolean() ?: false
+
     val entryPoint = config.getSpaceSeparated("entryPoint").singleOrNull()
     val linkerOpts = 
         config.getSpaceSeparated("linkerOpts").toTypedArray() +
@@ -285,7 +287,7 @@ private fun processLib(konanHome: String,
 
     val libName = fqParts.joinToString("") + "stubs"
 
-    val library = NativeLibrary(headerFiles, compilerOpts, language)
+    val library = NativeLibrary(headerFiles, compilerOpts, language, excludeSystemLibs)
     val configuration = InteropConfiguration(
             library = library,
             pkgName = outKtPkg,