A roadblock to the development of stand-alone microscale biomedical and chemical analysis systems is the relatively high heating power requirement of the microscale reactors, which typically exceeds the capability of low cost batteries. In this study, a microchannel thermal cycling reactor design using in-channel heating and passive cooling is proposed and a numerical model has been developed. Numerical simulations were conducted to determine the conditions under which efficient, rapid thermal cycling can be achieved with minimum heating power load. The simulations revealed that with a low thermal conductivity substrate and an optimized heater-channel configuration a microchannel reactor is capable of performing rapid thermal cycling to temperatures as high as 95 degreesC with as little as 20 mW/channel peak heating power.