Index: src/select.c
==================================================================
--- src/select.c
+++ src/select.c
@@ -4001,16 +4001,16 @@
 ** should be freed along with the Parse object. In other cases, when
 ** bFree==0, the With object will be freed along with the SELECT 
 ** statement with which it is associated.
 */
 void sqlite3WithPush(Parse *pParse, With *pWith, u8 bFree){
-  assert( bFree==0 || pParse->pWith==0 );
+  assert( bFree==0 || (pParse->pWith==0 && pParse->pWithToFree==0) );
   if( pWith ){
     assert( pParse->pWith!=pWith );
     pWith->pOuter = pParse->pWith;
     pParse->pWith = pWith;
-    pParse->bFreeWith = bFree;
+    if( bFree ) pParse->pWithToFree = pWith;
   }
 }
 
 /*
 ** This function checks if argument pFrom refers to a CTE declared by 
@@ -4099,10 +4099,11 @@
 
     pCte->zCteErr = "circular reference: %s";
     pSavedWith = pParse->pWith;
     pParse->pWith = pWith;
     sqlite3WalkSelect(pWalker, bMayRecursive ? pSel->pPrior : pSel);
+    pParse->pWith = pWith;
 
     for(pLeft=pSel; pLeft->pPrior; pLeft=pLeft->pPrior);
     pEList = pLeft->pEList;
     if( pCte->pCols ){
       if( pEList && pEList->nExpr!=pCte->pCols->nExpr ){

Index: src/sqliteInt.h
==================================================================
--- src/sqliteInt.h
+++ src/sqliteInt.h
@@ -2752,11 +2752,10 @@
   ************************************************************************/
 
   int nVar;                 /* Number of '?' variables seen in the SQL so far */
   int nzVar;                /* Number of available slots in azVar[] */
   u8 iPkSortOrder;          /* ASC or DESC for INTEGER PRIMARY KEY */
-  u8 bFreeWith;             /* True if pWith should be freed with parser */
   u8 explain;               /* True if the EXPLAIN flag is found on the query */
 #ifndef SQLITE_OMIT_VIRTUALTABLE
   u8 declareVtab;           /* True if inside sqlite3_declare_vtab() */
   int nVtabLock;            /* Number of virtual tables to lock */
 #endif
@@ -2779,10 +2778,11 @@
   Table **apVtabLock;       /* Pointer to virtual tables needing locking */
 #endif
   Table *pZombieTab;        /* List of Table objects to delete after code gen */
   TriggerPrg *pTriggerPrg;  /* Linked list of coded triggers */
   With *pWith;              /* Current WITH clause, or NULL */
+  With *pWithToFree;        /* Free this WITH object at the end of the parse */
 };
 
 /*
 ** Return true if currently inside an sqlite3_declare_vtab() call.
 */

Index: src/tokenize.c
==================================================================
--- src/tokenize.c
+++ src/tokenize.c
@@ -508,11 +508,11 @@
     ** will take responsibility for freeing the Table structure.
     */
     sqlite3DeleteTable(db, pParse->pNewTable);
   }
 
-  if( pParse->bFreeWith ) sqlite3WithDelete(db, pParse->pWith);
+  sqlite3WithDelete(db, pParse->pWithToFree);
   sqlite3DeleteTrigger(db, pParse->pNewTrigger);
   for(i=pParse->nzVar-1; i>=0; i--) sqlite3DbFree(db, pParse->azVar[i]);
   sqlite3DbFree(db, pParse->azVar);
   while( pParse->pAinc ){
     AutoincInfo *p = pParse->pAinc;

ADDED   test/with3.test
Index: test/with3.test
==================================================================
--- /dev/null
+++ test/with3.test
@@ -0,0 +1,64 @@
+# 2015-11-07
+#
+# 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 regression tests for SQLite library.  The
+# focus of this file is testing the WITH clause.
+#
+
+set testdir [file dirname $argv0]
+source $testdir/tester.tcl
+set ::testprefix with3
+
+ifcapable {!cte} {
+  finish_test
+  return
+}
+
+# Test problems found by Kostya Serebryany using 
+# LibFuzzer.  (http://llvm.org/docs/LibFuzzer.html)
+#
+do_catchsql_test 1.0 {
+  WITH i(x) AS (
+    WITH j AS (SELECT 10)
+    SELECT 5 FROM t0 UNION SELECT 8 FROM m
+  )
+  SELECT * FROM i;
+} {1 {no such table: m}}
+
+# Additional test cases that came out of the work to
+# fix for Kostya's problem.
+#
+do_execsql_test 2.0 {
+ WITH
+  x1 AS (SELECT 10),
+  x2 AS (SELECT 11),
+  x3 AS (
+    SELECT * FROM x1 UNION ALL SELECT * FROM x2
+  ),
+  x4 AS (
+    WITH
+    x1 AS (SELECT 12),
+    x2 AS (SELECT 13)
+    SELECT * FROM x3
+  )
+  SELECT * FROM x4;
+
+} {10 11}
+
+do_execsql_test 2.1 {
+  CREATE TABLE t1(x);
+  WITH
+    x1(a) AS (values(100))
+  INSERT INTO t1(x)
+    SELECT * FROM (WITH x2(y) AS (SELECT * FROM x1) SELECT y+a FROM x1, x2);
+  SELECT * FROM t1;
+} {200}
+
+finish_test