diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 4bb14e25c..12c893da8 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -196,6 +196,9 @@ public class GenomeAnalysisEngine {
         // our microscheduler, which is in charge of running everything
         MicroScheduler microScheduler = createMicroscheduler();
 
+        // create temp directories as necessary
+        initializeTempDirectory();
+
         // create the output streams                     "
         initializeOutputStreams(microScheduler.getOutputTracker());
 
@@ -473,6 +476,14 @@ public class GenomeAnalysisEngine {
         return walker instanceof ReadWalker;
     }
 
+    /**
+     * Create the temp directory if it doesn't exist.
+     */
+    private void initializeTempDirectory() {
+        File tempDir = new File(System.getProperty("java.io.tmpdir"));
+        tempDir.mkdirs();
+    }
+
     /**
      * Initialize the output streams as specified by the user.
      *