The present invention relates to a thermal cycler for the carrying out of chemical or biological reactions, such as PCR or other nucleic acid amplification reactions, that is segmented with a plurality of reaction vessel receiving elements. The reaction vessel receiving elements are thermally isolated from each other and provide an airtight seal to prevent liquids or moisture from penetrating below the reaction vessel receiving elements. The reaction vessel receiving elements have several recesses arranged in a pattern to receive the reaction vessels of a single standard microtiter plate and the segmented thermal cycler has a system for independently heating and cooling each of the reaction vessel receiving elements.