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 c159cc12eb3..9cafab38858 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
@@ -20,6 +20,8 @@ import clang.*
 import kotlinx.cinterop.*
 import java.io.Closeable
 import java.io.File
+import java.nio.file.Files
+import java.nio.file.Path
 import java.nio.file.Paths
 import java.security.DigestInputStream
 import java.security.MessageDigest
@@ -542,3 +544,58 @@ internal fun CValue<CXSourceLocation>.getContainingFile(): CXFile? = memScoped {
     clang_getFileLocation(this@getContainingFile, fileVar.ptr, null, null, null)
     fileVar.value
 }
+
+private fun createVfsOverlayFileContents(virtualPathToReal: Map<Path, Path>): ByteArray {
+    val overlay = clang_VirtualFileOverlay_create(0)
+
+    try {
+        fun addFileMapping(realPath: Path, virtualPath: Path) {
+            clang_VirtualFileOverlay_addFileMapping(
+                    overlay,
+                    virtualPath = virtualPath.toAbsolutePath().toString(),
+                    realPath = realPath.toAbsolutePath().toString()
+            )
+        }
+
+        virtualPathToReal.forEach { virtualPath, realPath ->
+            if (Files.isDirectory(realPath)) {
+                realPath.toFile().walkTopDown().forEach {
+                    if (!it.isDirectory) {
+                        addFileMapping(
+                                realPath = it.toPath(),
+                                virtualPath = virtualPath.resolve(realPath.relativize(it.toPath()))
+                        )
+                    }
+                }
+            } else {
+                addFileMapping(realPath = realPath, virtualPath = virtualPath)
+            }
+        }
+
+        memScoped {
+            val bufferVar = alloc<CPointerVar<ByteVar>>().apply { value = null }
+            val bufferSizeVar = alloc<IntVar>()
+
+            val res = clang_VirtualFileOverlay_writeToBuffer(overlay, 0, bufferVar.ptr, bufferSizeVar.ptr)
+            if (res != CXErrorCode.CXError_Success) {
+                // TODO: shall we free the buffer in this case?
+                error(res)
+            }
+
+            return bufferVar.value!!.readBytes(bufferSizeVar.value)
+        }
+    } finally {
+        clang_VirtualFileOverlay_dispose(overlay)
+    }
+}
+
+fun createVfsOverlayFile(virtualPathToReal: Map<Path, Path>): Path {
+    val bytes = createVfsOverlayFileContents(virtualPathToReal)
+
+    return createTempFile(prefix = "konan", suffix = ".vfsoverlay").apply {
+        bufferedWriter().use {
+            writeBytes(bytes)
+        }
+        deleteOnExit()
+    }.toPath()
+}
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 8f9dd4452cd..de10bb07ee3 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
@@ -23,8 +23,8 @@ import org.jetbrains.kotlin.native.interop.gen.ImportsImpl
 import org.jetbrains.kotlin.native.interop.indexer.*
 import java.io.File
 import java.lang.IllegalArgumentException
+import java.nio.file.*
 import java.util.*
-import kotlin.reflect.KFunction
 
 fun main(args: Array<String>) = interop(args, null)
 
@@ -211,6 +211,55 @@ private fun parseImports(args: Map<String, List<String>>): ImportsImpl {
     return ImportsImpl(headerIdToPackage)
 }
 
+fun getCompilerFlagsForVfsOverlay(args: Map<String, List<String>>, def: DefFile): List<String> {
+    val relativeToRoot = mutableMapOf<Path, Path>() // TODO: handle clashes
+
+    val HEADER_FILTER_ADDITIONAL_SEARCH_PREFIX = "-headerFilterAdditionalSearchPrefix"
+
+    val filteredIncludeDirs = args[HEADER_FILTER_ADDITIONAL_SEARCH_PREFIX]?.map { Paths.get(it) }
+    if (filteredIncludeDirs != null) {
+        val headerFilterGlobs = def.config.headerFilter
+        if (headerFilterGlobs.isEmpty()) {
+            error("'$HEADER_FILTER_ADDITIONAL_SEARCH_PREFIX' option requires " +
+                    "'headerFilter' to be specified in .def file")
+        }
+
+        relativeToRoot += findFilesByGlobs(roots = filteredIncludeDirs, globs = headerFilterGlobs)
+    }
+
+    if (relativeToRoot.isEmpty()) {
+        return emptyList()
+    }
+
+    val virtualRoot = Paths.get(System.getProperty("java.io.tmpdir")).resolve("konanSystemInclude")
+
+    val virtualPathToReal = relativeToRoot.map { (relativePath, realRoot) ->
+        virtualRoot.resolve(relativePath) to realRoot.resolve(relativePath)
+    }.toMap()
+
+    val vfsOverlayFile = createVfsOverlayFile(virtualPathToReal)
+
+    return listOf("-I${virtualRoot.toAbsolutePath()}", "-ivfsoverlay", vfsOverlayFile.toAbsolutePath().toString())
+}
+
+private fun findFilesByGlobs(roots: List<Path>, globs: List<String>): Map<Path, Path> {
+    val relativeToRoot = mutableMapOf<Path, Path>()
+
+    val pathMatchers = globs.map { FileSystems.getDefault().getPathMatcher("glob:$it") }
+
+    roots.reversed().forEach { root ->
+        // TODO: don't scan the entire tree, skip subdirectories according to globs.
+        Files.walk(root, FileVisitOption.FOLLOW_LINKS).forEach { path ->
+            val relativePath = root.relativize(path)
+            if (!Files.isDirectory(path) && pathMatchers.any { it.matches(relativePath) }) {
+                relativeToRoot[relativePath] = root
+            }
+        }
+    }
+    return relativeToRoot
+}
+
+
 private fun processLib(args: Map<String, List<String>>, 
                        argsToCompiler: MutableList<String>?) {
 
@@ -250,6 +299,7 @@ private fun processLib(args: Map<String, List<String>>,
         addAll(def.config.compilerOpts)
         addAll(tool.defaultCompilerOpts)
         addAll(additionalCompilerOpts)
+        addAll(getCompilerFlagsForVfsOverlay(args, def))
         addAll(when (language) {
             Language.C -> emptyList()
             Language.OBJECTIVE_C -> {