Abstract: A system is provided for carrying out rapid nucleic acid amplification or other biological reactions requiring thermal cycling. The system of this invention incorporates at least two heating blocks, each having a groove for receiving a reaction vessel such that only a portion of the outer surface of the walls of the vessel are in direct contact with the heating block. The remaining portion of the outer surface of the walls of the reaction vessel remains exposed to ambient conditions. The reaction vessel comes into contact with only one heating block at a time either by movement of the vessel between the heating blocks or by movement of the heating blocks in relation to the vessel. The system of this invention provides rapid temperature cycling without the need for extended ramping times generally associated with single block designs, which include a single temperature block that is forced to heat and cool.