Methods and apparatus for effecting rapid thermocycling in connection with the polymerase chain reaction are disclosed. A sample assembly having a relatively small thermal mass is heated to desired PCR operating temperatures, and a separate cooling assembly is used to rapidly lower the temperature as required. In one embodiment, a sample assembly with an integrated heating element is isolated from a relatively large thermal mass cold sink when the temperature of a sample is to be raised or maintained, and brought in contact with the cold sink when the temperature is desired to be lowered.