To better understand the role of the nuclear matrix in heat-induced cell killing, we have investigated the effects of heat shock on DNA replication complexes. Changes in protein extractability are observed following heat shock, including stabilization of which stabilize DNA replication complexes in association with the nuclear matrix. This situation is accompanied by differential delays in the progress and completion of DNA synthesis and the transition from type I to type II DNA replication patterns. Interestingly, prolonged delays in restarting DNA synthesis produced significant protection from heat-induced cell killing. These results show that nuclear matrix-associated DNA replication complexes may be important targets for heat-induced cell killing.