diff --git a/src/main/java/picard/sam/SamToFastq.java b/src/main/java/picard/sam/SamToFastq.java
index 668ff1ced..da217277a 100755
--- a/src/main/java/picard/sam/SamToFastq.java
+++ b/src/main/java/picard/sam/SamToFastq.java
@@ -84,20 +84,25 @@
     public File INPUT;
 
     @Option(shortName = "F", doc = "Output FASTQ file (single-end fastq or, if paired, first end of the pair FASTQ).",
-            mutex = {"OUTPUT_PER_RG"})
+            mutex = {"OUTPUT_PER_RG", "COMPRESS_OUTPUTS_PER_RG"})
     public File FASTQ;
 
     @Option(shortName = "F2", doc = "Output FASTQ file (if paired, second end of the pair FASTQ).", optional = true,
-            mutex = {"OUTPUT_PER_RG"})
+            mutex = {"OUTPUT_PER_RG", "COMPRESS_OUTPUTS_PER_RG"})
     public File SECOND_END_FASTQ;
 
-    @Option(shortName = "FU", doc = "Output FASTQ file for unpaired reads; may only be provided in paired-FASTQ mode", optional = true, mutex = {"OUTPUT_PER_RG"})
+    @Option(shortName = "FU", doc = "Output FASTQ file for unpaired reads; may only be provided in paired-FASTQ mode", optional = true,
+            mutex = {"OUTPUT_PER_RG", "COMPRESS_OUTPUTS_PER_RG"})
     public File UNPAIRED_FASTQ;
 
     @Option(shortName = "OPRG", doc = "Output a FASTQ file per read group (two FASTQ files per read group if the group is paired).",
             optional = true, mutex = {"FASTQ", "SECOND_END_FASTQ", "UNPAIRED_FASTQ"})
     public boolean OUTPUT_PER_RG;
 
+    @Option(shortName = "GZOPRG", doc = "Compress output FASTQ files per read group using gzip and append a .gz extension to the file names.",
+            optional = false, mutex = {"FASTQ", "SECOND_END_FASTQ", "UNPAIRED_FASTQ"})
+    public Boolean COMPRESS_OUTPUTS_PER_RG = false;
+
     @Option(shortName="RGT", doc = "The read group tag (PU or ID) to be used to output a FASTQ file per read group.")
     public String RG_TAG = "PU";
 
@@ -285,7 +290,7 @@ private File makeReadGroupFile(final SAMReadGroupRecord readGroup, final String
         }
         fileName = IOUtil.makeFileNameSafe(fileName);
         if (preExtSuffix != null) fileName += preExtSuffix;
-        fileName += ".fastq";
+        fileName += COMPRESS_OUTPUTS_PER_RG ? ".fastq.gz" : ".fastq";
 
         final File result = (OUTPUT_DIR != null)
                 ? new File(OUTPUT_DIR, fileName)
diff --git a/src/test/java/picard/sam/SamToFastqTest.java b/src/test/java/picard/sam/SamToFastqTest.java
index c0464e961..834f6a665 100644
--- a/src/test/java/picard/sam/SamToFastqTest.java
+++ b/src/test/java/picard/sam/SamToFastqTest.java
@@ -38,6 +38,7 @@
 import picard.PicardException;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -451,10 +452,44 @@ else if (record.getSecondOfPairFlag()) {
         }
     }
 
-    private File newTempFastqFile(final String filename) throws IOException {
+    private File newTempFastqFile(final String filename, final String suffix) throws IOException {
         if(filename == null) return null;
-        final File file = File.createTempFile(filename,".fastq");
+        final File file = File.createTempFile(filename, suffix);
         file.deleteOnExit();
         return file; 
     }
+
+    private File newTempFastqFile(final String filename) throws IOException {
+        return newTempFastqFile(filename, ".fastq");
+    }
+
+    @Test(dataProvider =  "okFiles")
+    public void testFileCompression(final String samFilename) throws IOException {
+        final File samFile = new File(TEST_DATA_DIR,samFilename);
+        final File pair1File = newTempFastqFile("pair1", ".fastq.gz");
+        final File pair2File = newTempFastqFile("pair2", ".fastq.gz");
+
+        convertFile(new String[]{
+              "INPUT=" + samFile.getAbsolutePath(),
+              "FASTQ=" + pair1File.getAbsolutePath(),
+              "SECOND_END_FASTQ=" + pair2File.getAbsolutePath()
+        });
+
+        verifyFileIsGzCompressed(pair1File);
+        verifyFileIsGzCompressed(pair2File);
+        // Content verification. Picard automatically recognizes the compression from the .gz suffix
+        // (htsjdk.samtools.util.IOUtil#openFileForReading(java.nio.file.Path)).
+        verifyFastq(pair1File, pair2File, samFile);
+    }
+
+    private void verifyFileIsGzCompressed(final File file) throws IOException {
+        FileInputStream fis = new FileInputStream(file);
+        final byte[] expectedMagicNumber = { (byte) 0x1f, (byte) 0x8b};
+        byte[] observedMagicNumber = new byte[2];
+        fis.read(observedMagicNumber, 0, 2);
+        fis.close();
+        Assert.assertEquals(observedMagicNumber, expectedMagicNumber);
+    }
+
+
 }