diff --git a/public/java/src/org/broadinstitute/sting/gatk/samples/Sample.java b/public/java/src/org/broadinstitute/sting/gatk/samples/Sample.java
index d57668715..8d19eb246 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/samples/Sample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/samples/Sample.java
@@ -9,7 +9,7 @@ import java.util.Map;
 /**
  *
  */
-public class Sample implements java.io.Serializable {
+public class Sample implements Comparable<Sample> { // implements java.io.Serializable {
     final private String familyID, paternalID, maternalID;
     final private Gender gender;
     final private double quantitativePhenotype;
@@ -118,6 +118,11 @@ public class Sample implements java.io.Serializable {
         return gender;
     }
 
+    @Override
+    public int compareTo(final Sample sample) {
+        return ID.compareTo(sample.getID());
+    }
+
     @Override
     public String toString() {
         return String.format("Sample %s fam=%s dad=%s mom=%s gender=%s affection=%s qt=%s props=%s",
diff --git a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
index 5ba2252e4..2c63f93ff 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
@@ -4,7 +4,6 @@ import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import sun.reflect.generics.reflectiveObjects.NotImplementedException;
 
 import java.util.*;
 
@@ -139,30 +138,42 @@ public class SampleDB {
     //
     // --------------------------------------------------------------------------------
 
-    public Set<String> getFamilyIDs() {
-        throw new NotImplementedException();
+    /**
+     * Returns a sorted set of the family IDs in all samples (excluding null ids)
+     * @return
+     */
+    public final Set<String> getFamilyIDs() {
+        return getFamilies().keySet();
     }
 
-    public Map<String, Set<Sample>> getFamilies() {
-        throw new NotImplementedException();
+    /**
+     * Returns a map from family ID -> set of family members for all samples with
+     * non-null family ids
+     *
+     * @return
+     */
+    public final Map<String, Set<Sample>> getFamilies() {
+        final Map<String, Set<Sample>> families = new TreeMap<String, Set<Sample>>();
+
+        for ( final Sample sample : samples.values() ) {
+            final String famID = sample.getFamilyID();
+            if ( famID != null ) {
+                if ( ! families.containsKey(famID) )
+                    families.put(famID, new TreeSet<Sample>());
+                families.get(famID).add(sample);
+            }
+        }
+
+        return families;
     }
 
     /**
      * Return all samples with a given family ID
-     * Note that this isn't terribly efficient (linear) - it may be worth adding a new family ID data structure for this
      * @param familyId
      * @return
      */
     public Set<Sample> getFamily(String familyId) {
-        HashSet<Sample> familyMembers = new HashSet<Sample>();
-
-        for (Sample sample : samples.values()) {
-            if (sample.getFamilyID() != null) {
-                if (sample.getFamilyID().equals(familyId))
-                    familyMembers.add(sample);
-            }
-        }
-        return familyMembers;
+        return getFamilies().get(familyId);
     }
 
     /**
@@ -172,9 +183,9 @@ public class SampleDB {
      * @return
      */
     public Set<Sample> getChildren(Sample sample) {
-        HashSet<Sample> children = new HashSet<Sample>();
-        for (Sample familyMember : getFamily(sample.getFamilyID())) {
-            if (familyMember.getMother() == sample || familyMember.getFather() == sample) {
+        final HashSet<Sample> children = new HashSet<Sample>();
+        for ( final Sample familyMember : getFamily(sample.getFamilyID())) {
+            if ( familyMember.getMother() == sample || familyMember.getFather() == sample ) {
                 children.add(familyMember);
             }
         }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
index b6b4fab54..d498ee61a 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
@@ -9,9 +9,7 @@ import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 import java.io.File;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.Set;
+import java.util.*;
 
 /**
  * Created by IntelliJ IDEA.
@@ -36,9 +34,17 @@ public class SampleDBUnitTest extends BaseTest {
 
     private static final String testPEDString =
             String.format("%s%n%s%n%s",
-                        "fam1 kid dad mom 1 2",
-                        "fam1 dad 0   0   1 1",
-                        "fam1 mom 0   0   2 2");
+                    "fam1 kid dad mom 1 2",
+                    "fam1 dad 0   0   1 1",
+                    "fam1 mom 0   0   2 2");
+
+    private static final String testPEDMultipleFamilies =
+            String.format("%s%n%s%n%s%n%s%n%s",
+                    "fam1 kid dad mom 1 2",
+                    "fam1 dad 0   0   1 1",
+                    "fam1 mom 0   0   2 2",
+                    "fam3 s1  d1  m1  2 2",
+                    "fam2 s2  d2  m2  2 2");
 
     private static final String testPEDStringInconsistentGender =
             "fam1 kid 0   0   2 2";
@@ -117,4 +123,35 @@ public class SampleDBUnitTest extends BaseTest {
         builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDStringInconsistentGender));
         builder.getFinalSampleDB();
     }
+
+    @Test()
+    public void getFamilyIDs() {
+        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));
+        SampleDB db = builder.getFinalSampleDB();
+        Assert.assertEquals(db.getFamilyIDs(), new TreeSet<String>(Arrays.asList("fam1", "fam2", "fam3")));
+    }
+
+    @Test()
+    public void getFamily() {
+        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));
+        SampleDB db = builder.getFinalSampleDB();
+        Assert.assertEquals(db.getFamily("fam1"), testPEDSamplesAsSet);
+    }
+
+    @Test()
+    public void loadFamilyIDs() {
+        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));
+        SampleDB db = builder.getFinalSampleDB();
+        Map<String, Set<Sample>> families = db.getFamilies();
+        Assert.assertEquals(families.size(), 3);
+        Assert.assertEquals(families.keySet(), new TreeSet<String>(Arrays.asList("fam1", "fam2", "fam3")));
+
+        for ( final String famID : families.keySet() ) {
+            final Set<Sample> fam = families.get(famID);
+            Assert.assertEquals(fam.size(), 3);
+            for ( final Sample sample : fam ) {
+                Assert.assertEquals(sample.getFamilyID(), famID);
+            }
+        }
+    }
 }