Index: lucene/src/java/org/apache/lucene/search/BooleanQuery.java
===================================================================
--- lucene/src/java/org/apache/lucene/search/BooleanQuery.java	(revision 1174729)
+++ lucene/src/java/org/apache/lucene/search/BooleanQuery.java	(working copy)
@@ -179,6 +179,8 @@
       this.disableCoord = disableCoord;
       weights = new ArrayList<Weight>(clauses.size());
       boolean termConjunction = clauses.isEmpty() || minNrShouldMatch != 0 ? false : true;
+      int numProhibited = 0;
+      
       for (int i = 0 ; i < clauses.size(); i++) {
         BooleanClause c = clauses.get(i);
         Weight w = c.getQuery().createWeight(searcher);
@@ -186,8 +188,20 @@
           termConjunction = false;
         }
         weights.add(w);
-        if (!c.isProhibited()) maxCoord++;
+        if (c.isProhibited()) {
+          numProhibited++;
+        } else {
+          maxCoord++;
+        }
       }
+          
+      // check for only prohibited clauses
+      if (numProhibited > 0 && numProhibited == clauses.size()) {
+        throw new UnsupportedOperationException(
+          "A BooleanQuery must have at least one SHOULD or MUST clause, if MUST_NOT clauses are used."
+        );
+      }
+
       this.termConjunction = termConjunction;
     }
 
Index: modules/queries/src/java/org/apache/lucene/queries/BooleanFilter.java
===================================================================
--- modules/queries/src/java/org/apache/lucene/queries/BooleanFilter.java	(revision 1174729)
+++ modules/queries/src/java/org/apache/lucene/queries/BooleanFilter.java	(working copy)
@@ -35,8 +35,8 @@
  * SHOULD, MUST NOT, MUST
  * The results Filter BitSet is constructed as follows:
  * SHOULD Filters are OR'd together
+ * The resulting Filter is AND'd with the MUST Filters
  * The resulting Filter is NOT'd with the NOT Filters
- * The resulting Filter is AND'd with the MUST Filters
  */
 public class BooleanFilter extends Filter {
 
@@ -52,6 +52,18 @@
   public DocIdSet getDocIdSet(AtomicReaderContext context) throws IOException {
     FixedBitSet res = null;
     final IndexReader reader = context.reader;
+
+    int positiveClauseCount =
+      (shouldFilters != null ? shouldFilters.size() : 0) +
+      (mustFilters != null ? mustFilters.size() : 0);
+    int prohibitedClauseCount =
+      notFilters != null ? notFilters.size() : 0;
+    if (positiveClauseCount == 0 && prohibitedClauseCount > 0) {
+      throw new UnsupportedOperationException(
+        "A BooleanFilter must have at least one SHOULD or MUST clause, if MUST_NOT clauses are used."
+      );
+    }
+    
     if (shouldFilters != null) {
       for (int i = 0; i < shouldFilters.size(); i++) {
         final DocIdSetIterator disi = getDISI(shouldFilters, i, context);
@@ -63,19 +75,6 @@
       }
     }
     
-    if (notFilters != null) {
-      for (int i = 0; i < notFilters.size(); i++) {
-        if (res == null) {
-          res = new FixedBitSet(reader.maxDoc());
-          res.set(0, reader.maxDoc()); // NOTE: may set bits on deleted docs
-        }
-        final DocIdSetIterator disi = getDISI(notFilters, i, context);
-        if (disi != null) {
-          res.andNot(disi);
-        }
-      }
-    }
-    
     if (mustFilters != null) {
       for (int i = 0; i < mustFilters.size(); i++) {
         final DocIdSetIterator disi = getDISI(mustFilters, i, context);
@@ -91,6 +90,15 @@
       }
     }
 
+    // to apply NOT filters we need at least some matching docs (res != null)
+    if (res != null && notFilters != null) {
+      for (int i = 0; i < notFilters.size(); i++) {
+        final DocIdSetIterator disi = getDISI(notFilters, i, context);
+        if (disi == null) continue;
+        res.andNot(disi);
+      }
+    }
+    
     return res != null ? res : DocIdSet.EMPTY_DOCIDSET;
   }
 
@@ -120,7 +128,7 @@
   private DocIdSetIterator getDISI(List<Filter> filters, int index, AtomicReaderContext context)
       throws IOException {
     final DocIdSet set = filters.get(index).getDocIdSet(context);
-    return (set == null) ? null : set.iterator();
+    return (set == null || set == DocIdSet.EMPTY_DOCIDSET) ? null : set.iterator();
   }
   
   @Override
Index: modules/queries/src/test/org/apache/lucene/queries/BooleanFilterTest.java
===================================================================
--- modules/queries/src/test/org/apache/lucene/queries/BooleanFilterTest.java	(revision 1174729)
+++ modules/queries/src/test/org/apache/lucene/queries/BooleanFilterTest.java	(working copy)
@@ -225,12 +225,20 @@
   public void testJustMustNot() throws Throwable {
     BooleanFilter booleanFilter = new BooleanFilter();
     booleanFilter.add(new FilterClause(getTermsFilter("inStock", "N"), BooleanClause.Occur.MUST_NOT));
-    tstFilterCard("MUST_NOT", 4, booleanFilter);
+    try {
+      tstFilterCard("MUST_NOT", 0, booleanFilter);
+      fail("This must throw UnsupportedOperationException");
+    } catch (UnsupportedOperationException uoe) {
+    }
     
     // same with a real DISI (no OpenBitSetIterator)
     booleanFilter = new BooleanFilter();
     booleanFilter.add(new FilterClause(getWrappedTermQuery("inStock", "N"), BooleanClause.Occur.MUST_NOT));
-    tstFilterCard("MUST_NOT", 4, booleanFilter);
+    try {
+      tstFilterCard("MUST_NOT", 0, booleanFilter);
+      fail("This must throw UnsupportedOperationException");
+    } catch (UnsupportedOperationException uoe) {
+    }
   }
 
   public void testMustAndMustNot() throws Throwable {
@@ -297,10 +305,18 @@
     
     booleanFilter = new BooleanFilter();
     booleanFilter.add(new FilterClause(getNullDISFilter(), BooleanClause.Occur.MUST_NOT));
-    tstFilterCard("A single MUST_NOT filter that returns a null DIS should be invisible", 5, booleanFilter);
+    try {
+      tstFilterCard("MUST_NOT", 0, booleanFilter);
+      fail("This must throw UnsupportedOperationException");
+    } catch (UnsupportedOperationException uoe) {
+    }
     
     booleanFilter = new BooleanFilter();
     booleanFilter.add(new FilterClause(getNullDISIFilter(), BooleanClause.Occur.MUST_NOT));
-    tstFilterCard("A single MUST_NOT filter that returns a null DIS should be invisible", 5, booleanFilter);
+    try {
+      tstFilterCard("MUST_NOT", 0, booleanFilter);
+      fail("This must throw UnsupportedOperationException");
+    } catch (UnsupportedOperationException uoe) {
+    }
   }
 }