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Because many proteins useful in biosensors exhibit temperature dependent activity, this paper explores the opportunity to integrate thermal control within a protein array biosensor microsystem. A CMOS microhotplate array tailored to protein interfaces was developed for thermoregulation in a liquid sample environment. The microhotplates were shown to provide suitable thermal control for biosensor temperature ranges without the process complexity of most previously reported microhotplates. When combined with a CMOS analog thermal controller, the on-chip array was shown to set and hold temperatures for each protein site within ±1°C, and array elements were found to be almost completely thermally isolated from each other at distances beyond 0.4 mm. The compact size and low power of this controller enable it to be combined with the thermal control structures and instantiated for every element in a sensor array to increase biosensor interrogation throughput.