diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 51e39d768..aa746a757 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -676,8 +676,14 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 altIdx += elementLength;
                 break;
             case I:
-                for (int j = 0; j < elementLength; j++)
+                for (int j = 0; j < elementLength; j++) {
+                   if ( ! BaseUtils.isRegularBase(readStr[altIdx+j]) ) {
+                       // Insertions with N's in them cause real problems sometimes; it's better to drop them altogether
+                       ok_flag=false;
+                       break;
+                   }
                     sb.append((char)readStr[altIdx + j]);
+                }
                 altIdx += elementLength;
                 indelCount++;
                 break;