Index: src/where.c
==================================================================
--- src/where.c
+++ src/where.c
@@ -4608,12 +4608,12 @@
         /* Conditions under which this table becomes the best so far:
         **
         **   (1) The table must not depend on other tables that have not
         **       yet run.
         **
-        **   (2) A full-table-scan plan cannot supercede another plan unless
-        **       it is an "optimal" plan as defined above.
+        **   (2) A full-table-scan plan cannot supercede indexed plan unless
+        **       the full-table-scan is an "optimal" plan as defined above.
         **
         **   (3) All tables have an INDEXED BY clause or this table lacks an
         **       INDEXED BY clause or this table uses the specific
         **       index specified by its INDEXED BY clause.  This rule ensures
         **       that a best-so-far is always selected even if an impossible
@@ -4625,10 +4625,11 @@
         **   (4) The plan cost must be lower than prior plans or else the
         **       cost must be the same and the number of rows must be lower.
         */
         if( (sCost.used&notReady)==0                       /* (1) */
             && (bestJ<0 || (notIndexed&m)!=0               /* (2) */
+                || (bestPlan.plan.wsFlags & WHERE_NOT_FULLSCAN)==0
                 || (sCost.plan.wsFlags & WHERE_NOT_FULLSCAN)!=0)
             && (nUnconstrained==0 || pTabItem->pIndex==0   /* (3) */
                 || NEVER((sCost.plan.wsFlags & WHERE_NOT_FULLSCAN)!=0))
             && (bestJ<0 || sCost.rCost<bestPlan.rCost      /* (4) */
                 || (sCost.rCost<=bestPlan.rCost 

ADDED   test/analyze6.test
Index: test/analyze6.test
==================================================================
--- test/analyze6.test
+++ test/analyze6.test
@@ -0,0 +1,74 @@
+# 2011 March 3
+#
+# The author disclaims copyright to this source code.  In place of
+# a legal notice, here is a blessing:
+#
+#    May you do good and not evil.
+#    May you find forgiveness for yourself and forgive others.
+#    May you share freely, never taking more than you give.
+#
+#***********************************************************************
+#
+# This file implements tests for SQLite library.  The focus of the tests
+# in this file a corner-case query planner optimization involving the
+# join order of two tables of different sizes.
+#
+
+set testdir [file dirname $argv0]
+source $testdir/tester.tcl
+
+ifcapable !stat2 {
+  finish_test
+  return
+}
+
+set testprefix analyze6
+
+proc eqp {sql {db db}} {
+  uplevel execsql [list "EXPLAIN QUERY PLAN $sql"] $db
+}
+
+do_test analyze6-1.0 {
+  db eval {
+    CREATE TABLE cat(x INT);
+    CREATE UNIQUE INDEX catx ON cat(x);
+    /* Give cat 16 unique integers */
+    INSERT INTO cat VALUES(1);
+    INSERT INTO cat VALUES(2);
+    INSERT INTO cat SELECT x+2 FROM cat;
+    INSERT INTO cat SELECT x+4 FROM cat;
+    INSERT INTO cat SELECT x+8 FROM cat;
+
+    CREATE TABLE ev(y INT);
+    CREATE INDEX evy ON ev(y);
+    /* ev will hold 32 copies of 16 integers found in cat */
+    INSERT INTO ev SELECT x FROM cat;
+    INSERT INTO ev SELECT x FROM cat;
+    INSERT INTO ev SELECT y FROM ev;
+    INSERT INTO ev SELECT y FROM ev;
+    INSERT INTO ev SELECT y FROM ev;
+    INSERT INTO ev SELECT y FROM ev;
+    ANALYZE;
+    SELECT count(*) FROM cat;
+    SELECT count(*) FROM ev;
+  }
+} {16 512}
+
+# The lowest cost plan is to scan CAT and for each integer there, do a single
+# lookup of the first corresponding entry in EV then read off the equal values
+# in EV.  (Prior to the 2011-03-04 enhancement to where.c, this query would
+# have used EV for the outer loop instead of CAT - which was about 3x slower.)
+#
+do_test analyze6-1.1 {
+  eqp {SELECT count(*) FROM ev, cat WHERE x=y}
+} {0 0 1 {SCAN TABLE cat (~16 rows)} 0 1 0 {SEARCH TABLE ev USING COVERING INDEX evy (y=?) (~32 rows)}}
+
+# The same plan is chosen regardless of the order of the tables in the
+# FROM clause.
+#
+do_test analyze6-1.2 {
+  eqp {SELECT count(*) FROM cat, ev WHERE x=y}
+} {0 0 0 {SCAN TABLE cat (~16 rows)} 0 1 1 {SEARCH TABLE ev USING COVERING INDEX evy (y=?) (~32 rows)}}
+
+
+finish_test