diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
index 5b22138fb..1df847e17 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
@@ -101,6 +101,8 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
                     return new VectorLoglessPairHMM(VectorLoglessPairHMM.Implementation.AVX, pairHmmNativeArgs);
                 case VECTOR_LOGLESS_CACHING_OMP:
                     return new VectorLoglessPairHMM(VectorLoglessPairHMM.Implementation.OMP, pairHmmNativeArgs);
+                case VECTOR_LOGLESS_CACHING_FPGA_EXPERIMENTAL:
+                    return new VectorLoglessPairHMM(VectorLoglessPairHMM.Implementation.FPGA, pairHmmNativeArgs);
                 case FASTEST_AVAILABLE:
                     try {
                         return new VectorLoglessPairHMM(VectorLoglessPairHMM.Implementation.OMP, pairHmmNativeArgs);
@@ -125,7 +127,7 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
                 default:
                     throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or " +
                         "incompatible with the HaplotypeCaller. Acceptable options are ORIGINAL, EXACT, CACHING, LOGLESS_CACHING, " +
-                        "VECTOR_LOGLESS_CACHING, VECTOR_LOGLESS_CACHING_OMP, and ARRAY_LOGLESS.");
+                        "VECTOR_LOGLESS_CACHING, VECTOR_LOGLESS_CACHING_OMP, VECTOR_LOGLESS_CACHING_FPGA_EXPERIMENTAL, and ARRAY_LOGLESS.");
             }
         }
     };
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java
index d096bbf33..44b62262e 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java
@@ -53,6 +53,7 @@ package org.broadinstitute.gatk.utils.pairhmm;
 
 import com.intel.gkl.pairhmm.IntelPairHmm;
 import com.intel.gkl.pairhmm.IntelPairHmmOMP;
+import com.intel.gkl.pairhmm.IntelPairHmmFpga;
 import org.apache.log4j.Logger;
 import org.broadinstitute.gatk.nativebindings.pairhmm.HaplotypeDataHolder;
 import org.broadinstitute.gatk.nativebindings.pairhmm.PairHMMNativeArguments;
@@ -85,7 +86,9 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
         /* Use AVX acceleration */
         AVX,
         /* Use AVX acceleration with mult-threading via OpenMP */
-        OMP
+        OMP,
+        /* Use FPGA acceleration */
+        FPGA
     }
 
     protected final static Logger logger = Logger.getLogger(VectorLoglessPairHMM.class);
@@ -114,6 +117,15 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
                 logger.info("Using OpenMP multi-threaded AVX-accelerated native PairHMM implementation");
                 break;
 
+            case FPGA:
+                pairHmm = new IntelPairHmmFpga();
+                isSupported = pairHmm.load(null);
+                if (!isSupported) {
+                    throw new UserException.HardwareFeatureException("Machine does not support FPGA PairHMM.");
+                }
+                logger.info("Using FPGA-accelerated native PairHMM implementation");
+                break;
+
             default:
                 throw new UserException.HardwareFeatureException("Unknown PairHMM implementation.");
         }
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java
index fcad408c6..3105442a6 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java
@@ -64,6 +64,8 @@ public abstract class PairHMM {
         VECTOR_LOGLESS_CACHING,
         /* Optimized, multi-threaded AVX implementation of LOGLESS_CACHING called through JNI */
         VECTOR_LOGLESS_CACHING_OMP,
+        /* Optimized, FPGA implementation of LOGLESS_CACHING called through JNI. This is still experimental! */
+        VECTOR_LOGLESS_CACHING_FPGA_EXPERIMENTAL,
         /* Use fastest available implementation. OMP -> AVX -> LOGLESS_CACHING */
         FASTEST_AVAILABLE,
         /* Debugging for vector implementation of LOGLESS_CACHING */