diff --git a/core/src/main/scala/com/eed3si9n/jarjarabrams/Main.scala b/core/src/main/scala/com/eed3si9n/jarjarabrams/Main.scala
index 2070bda..b12f792 100644
--- a/core/src/main/scala/com/eed3si9n/jarjarabrams/Main.scala
+++ b/core/src/main/scala/com/eed3si9n/jarjarabrams/Main.scala
@@ -16,13 +16,15 @@ class Main {
       case Some(_) => java.lang.Boolean.getBoolean("resetTimestamp")
       case None    => true
     }
+    val warnOnDuplicateClass = java.lang.Boolean.getBoolean("duplicateClassToWarn")
     Shader.shadeFile(
       Shader.parseRulesFile(rulesFile),
       inJar,
       outJar,
       verbose,
       skipManifest,
-      resetTimestamp
+      resetTimestamp,
+      warnOnDuplicateClass
     )
   }
 }
diff --git a/core/src/main/scala/com/eed3si9n/jarjarabrams/Shader.scala b/core/src/main/scala/com/eed3si9n/jarjarabrams/Shader.scala
index 981cd87..f6cccaf 100644
--- a/core/src/main/scala/com/eed3si9n/jarjarabrams/Shader.scala
+++ b/core/src/main/scala/com/eed3si9n/jarjarabrams/Shader.scala
@@ -13,10 +13,11 @@ object Shader {
       outputJar: Path,
       verbose: Boolean,
       skipManifest: Boolean,
-      resetTimestamp: Boolean
+      resetTimestamp: Boolean,
+      warnOnDuplicateClass: Boolean
   ): Unit = {
     val shader = bytecodeShader(rules, verbose, skipManifest)
-    Zip.transformJarFile(inputJar, outputJar, resetTimestamp) { struct0 =>
+    Zip.transformJarFile(inputJar, outputJar, resetTimestamp, warnOnDuplicateClass) { struct0 =>
       shader(struct0.data, struct0.name).map {
         case (shadedBytes, shadedName) =>
           Zip.entryStruct(shadedName, struct0.time, shadedBytes, struct0.skipTransform)
diff --git a/core/src/main/scala/com/eed3si9n/jarjarabrams/Zip.scala b/core/src/main/scala/com/eed3si9n/jarjarabrams/Zip.scala
index 672d0a9..1bc3df5 100644
--- a/core/src/main/scala/com/eed3si9n/jarjarabrams/Zip.scala
+++ b/core/src/main/scala/com/eed3si9n/jarjarabrams/Zip.scala
@@ -1,6 +1,6 @@
 package com.eed3si9n.jarjarabrams
 
-import com.eed3si9n.jarjar.util.EntryStruct
+import com.eed3si9n.jarjar.util.{ DuplicateJarEntryException, EntryStruct }
 import java.nio.file.{ Files, NoSuchFileException, Path, StandardCopyOption }
 import java.nio.file.attribute.FileTime
 import java.io.{ ByteArrayOutputStream, FileNotFoundException, InputStream, OutputStream }
@@ -46,7 +46,8 @@ object Zip {
   def transformJarFile(
       inputJar: Path,
       outputJar: Path,
-      resetTimestamp: Boolean
+      resetTimestamp: Boolean,
+      warnOnDuplicateClass: Boolean
   )(f: EntryStruct => Option[EntryStruct]): Path =
     Using.jarFile(inputJar) { in =>
       val tempJar = Files.createTempFile("jarjar", ".jar")
@@ -72,8 +73,11 @@ object Zip {
                 out.write(struct.data)
               } else if (struct.name.endsWith("/")) ()
               else {
-                // duplicate entry
-                // throw?
+                if (warnOnDuplicateClass)
+                  Console.err.println(
+                    s"in ${inputJar}, found duplicate files with name: ${struct.name}, ignoring due to specified option"
+                  )
+                else throw new DuplicateJarEntryException(inputJar.toString, struct.name)
               }
             case None => ()
           }
diff --git a/core/src/test/scala/testpkg/ShaderTest.scala b/core/src/test/scala/testpkg/ShaderTest.scala
index f20d04d..9247516 100644
--- a/core/src/test/scala/testpkg/ShaderTest.scala
+++ b/core/src/test/scala/testpkg/ShaderTest.scala
@@ -60,7 +60,8 @@ object ShaderTest extends BasicTestSuite {
       tempJar,
       verbose = false,
       skipManifest = false,
-      resetTimestamp
+      resetTimestamp,
+      warnOnDuplicateClass = false
     )
     val entries = Zip.list(tempJar).map(_._1)
     assert(entries.contains(expectedClass))