diff --git a/etc/log4j.properties b/etc/log4j.properties
index b70338f3181ecbabf224c77f5fbb6661ae92c4a1..c36f3d9b0dd7f445798bddf74e956274b1ba4e3f 100644
--- a/etc/log4j.properties
+++ b/etc/log4j.properties
@@ -31,7 +31,7 @@ log4j.logger.uk.ac.sanger.artemis.components.genebuilder.cv.GoBox=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.chado.ArtemisUtils=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.components.database.DatabaseJPanel=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.components.alignment.LookSeqPanel=DEBUG, R
-log4j.logger.uk.ac.sanger.artemis.components.variant.BCFReader=DEBUG, R
+log4j.logger.uk.ac.sanger.artemis.components.variant=DEBUG, stdout, R
 log4j.logger.uk.ac.sanger.artemis.io.ReadAndWriteEntry=DEBUG, R
 log4j.logger.uk.ac.sanger.artemis.util.FTPSeekableStream=DEBUG, R
 
diff --git a/uk/ac/sanger/artemis/components/variant/VCFRecord.java b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
index 543ba1fbe4a78c3cdc79508a4d4441bd36e431f7..d13008e75f0eb5f2bbf0aaeadceceacf55bdd15e 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFRecord.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
@@ -398,8 +398,8 @@ public class VCFRecord
   
   protected static short checkSyn(CDSFeature gfeat, int basePosition, char variant)
   {
-    System.out.println("CDSFEATURE\t"+gfeat);
-    System.out.println("BASEANDVARIANT\t"+basePosition + "\t" + variant);
+    logger.info("CDSFEATURE\t"+gfeat);
+    logger.info("BASEANDVARIANT\t"+basePosition + "\t" + variant);
     if(gfeat.firstBase < basePosition && gfeat.lastBase > basePosition)
     {
       RangeVector ranges = gfeat.ranges;
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index e9e1f8ae6f1daffa71f899cdab4c971eaec499e2..d0af0a9b4ea126097b99fbff607e9219b9a624f0 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -1089,7 +1089,7 @@ public class VCFview extends JPanel
     try
     {
       VCFRecord record;
-      System.out.println(
+      logger.info(
               String.format(
               "FILTER\t%s-%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
               sbeg, 
@@ -1204,7 +1204,7 @@ public class VCFview extends JPanel
     
     short isSyn = -1;
     isSyn = record.getSynFlag(features, basePosition);
-    System.out.println("ISSYNONYMOUS\t"+record.getPos() +"\t" + isSyn);
+    logger.info("ISSYNONYMOUS\t"+record.getPos() +"\t" + isSyn);
     markAsNewStop = false;
     if(markNewStops.isSelected() &&
        !record.getAlt().isDeletion(vcf_v4) && 
@@ -1261,7 +1261,7 @@ public class VCFview extends JPanel
   {
     int basePosition = record.getPos() + getSequenceOffset(record.getChrom());
     boolean show = showVariant(record, features, basePosition, vcf_v4);
-    System.out.println(String.format("%s\t%s", (show) ? "SHOW" : "HIDE", record));
+    logger.info(String.format("%s\t%s", (show) ? "SHOW" : "HIDE", record));
     if( !show )
       return;