diff --git a/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/highlighter2/Html2CompilerPlugin.kt b/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/highlighter2/Html2CompilerPlugin.kt
index 6a90073e8f4..6288548d811 100644
--- a/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/highlighter2/Html2CompilerPlugin.kt
+++ b/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/highlighter2/Html2CompilerPlugin.kt
@@ -18,6 +18,7 @@ import org.jetbrains.jet.lexer.JetTokens
 import org.jetbrains.kotlin.doc.Doclet
 import org.jetbrains.kotlin.doc.model.KModel
 import org.jetbrains.jet.lang.psi.JetFile
+import org.jetbrains.kotlin.doc.model.SourceInfo
 
 
 class Html2CompilerPlugin(private val compilerArguments: KDocArguments) : Doclet {
@@ -65,14 +66,15 @@ class Html2CompilerPlugin(private val compilerArguments: KDocArguments) : Doclet
             #()
         }
 
-        for (file in model.sources) {
-            processFile(file)
+        for (sourceInfo in model.sourcesInfo) {
+            processFile(sourceInfo)
         }
     }
 
-    private fun processFile(psiFile: JetFile) {
-        val relativePath = fileToWrite(psiFile)
-        val htmlFile = File(srcOutputRoot, relativePath.replaceFirst("\\.kt$", "") + ".html")
+    private fun processFile(sourceInfo: SourceInfo) {
+        val psiFile = sourceInfo.psi
+        val htmlPath = sourceInfo.htmlPath
+        val htmlFile = File(srcOutputRoot, htmlPath)
 
         println("Generating $htmlFile")
         htmlFile.getParentFile()!!.mkdirs()
diff --git a/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/model/KModelCompilerPlugin.kt b/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/model/KModelCompilerPlugin.kt
index dd2fbfee013..d7e113f3cf2 100644
--- a/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/model/KModelCompilerPlugin.kt
+++ b/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/model/KModelCompilerPlugin.kt
@@ -4,6 +4,8 @@ import org.jetbrains.jet.cli.common.CompilerPlugin
 import org.jetbrains.jet.cli.common.CompilerPluginContext
 import org.jetbrains.kotlin.doc.KDocConfig
 import org.jetbrains.kotlin.doc.KDocArguments
+import java.io.File
+import java.util.List
 
 /** Base class for any compiler plugin which needs to process a KModel */
 abstract class KModelCompilerPlugin(
@@ -16,7 +18,8 @@ abstract class KModelCompilerPlugin(
     public override fun processFiles(context: CompilerPluginContext) {
         val bindingContext = context.getContext()
         val sources = context.getFiles()
-        val model = KModel(bindingContext, arguments.apply(), sources.requireNoNulls())
+        val sourceDirs: List<File> = arguments.getSourceDirs().orEmpty().requireNoNulls().map { path -> File(path) }
+        val model = KModel(bindingContext, arguments.apply(), sourceDirs, sources.requireNoNulls())
 
         processModel(model)
     }
diff --git a/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/model/KotlinModel.kt b/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/model/KotlinModel.kt
index 136f3a91616..9e68d1bdfd2 100644
--- a/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/model/KotlinModel.kt
+++ b/libraries/tools/kdoc/src/main/kotlin/org/jetbrains/kotlin/doc/model/KotlinModel.kt
@@ -44,6 +44,7 @@ import org.jetbrains.jet.lang.diagnostics.DiagnosticUtils.LineAndColumn
 import org.jetbrains.jet.internal.com.intellij.psi.PsiFileSystemItem
 import java.io.File
 import org.jetbrains.jet.internal.com.intellij.psi.PsiElement
+import org.jetbrains.jet.internal.com.intellij.openapi.vfs.local.CoreLocalVirtualFile
 
 
 /**
@@ -175,7 +176,10 @@ abstract class KClassOrPackage(model: KModel, declarationDescriptor: Declaration
     }
 }
 
-class KModel(val context: BindingContext, val config: KDocConfig, val sources: List<JetFile>) {
+// htmlPath does not include "html-src" prefix
+class SourceInfo(val psi: JetFile, val relativePath: String, val htmlPath: String)
+
+class KModel(val context: BindingContext, val config: KDocConfig, val sourceDirs: List<File>, val sources: List<JetFile>) {
     // TODO generates java.lang.NoSuchMethodError: kotlin.util.namespace.hashMap(Ljet/TypeInfo;Ljet/TypeInfo;)Ljava/util/HashMap;
     //val packages = sortedMap<String,KPackage>()
     public val packageMap: SortedMap<String, KPackage> = TreeMap<String, KPackage>()
@@ -236,9 +240,35 @@ class KModel(val context: BindingContext, val config: KDocConfig, val sources: L
         }
     }
 
+
+    val sourcesInfo: List<SourceInfo>
+    ;{
+
+        val normalizedSourceDirs: List<String> =
+            sourceDirs.map { file -> file.getCanonicalPath()!! }
+
+        private fun relativePath(psiFile: PsiFile): String {
+            val file = File((psiFile.getVirtualFile() as CoreLocalVirtualFile).getPath()).getCanonicalFile()!!
+            val filePath = file.getPath()!!
+            for (sourceDirPath in normalizedSourceDirs) {
+                if (filePath.startsWith(sourceDirPath) && filePath.length() > sourceDirPath.length()) {
+                    return filePath.substring(sourceDirPath.length + 1)
+                }
+            }
+            throw Exception("$file is not a child of any source roots $normalizedSourceDirs")
+        }
+
+        sourcesInfo = sources.map { source ->
+            val relativePath = relativePath(source)
+            val htmlPath = relativePath.replaceFirst("\\.kt$", "") + ".html"
+            SourceInfo(source, relativePath, htmlPath)
+        }
+    }
+
+
     /**
-     * Returns the root project directory for calculating relative source links
-     */
+    * Returns the root project directory for calculating relative source links
+    */
     fun projectRootDir(): String {
         if (_projectRootDir == null) {
             val rootDir = config.projectRootDir