Design and fabrication of a Silicon-based MEMS rotary engine are discussed in this paper. This work is part of an effort currently underway to develop a portable, autonomous power generation system potentially capable of having an order of magnitude improvement in energy density over alkaline or lithium-ion batteries. Central to the development of this power generation system are small-scale rotary internal combustion engines fueled by high energy density liquid hydrocarbons capable of delivering power on the order of milli-Watts. The rotary (Wankel-type) engine is well suited for MEMS fabrication due to its planar geometry, high specific power, and self-valving operation with a minimal number of moving parts. The smallest “micro-rotary” engine currently being fabricated has an epitrochoidal-shaped housing under 1 mm3 in size and with a rotor swept volume of 0.08 mm3. This paper discusses some of the fabrication issues unique to MEMS fabrication of a rotary engine at this small scale. High precision, high aspect ratio structures are necessary to provide adequate sealing for high compression ratios. Effects such as footing and lateral to vertical etch rates must be minimized for proper engine operation. A fabrication process is necessary for the complex, multi-height geometry of the housing and rotor assembly. Finally, a repeatable and simple assembly technique must be developed in order to mass-produce these engines. Fabrication of a Silicon-based micro-rotary engine is being conducted in U.C. Berkeley’s Microfabrication Laboratory. The engine system is composed of three main components: rotor, housing, and shaft. The engine and rotor housing must be entirely fabricated from Silicon without embedded oxide to prevent thermal mismatch or structural weakness at the Si-oxide interface. In order to meet this requirement, the fabrication processes for the housing consists of a two-mask two-etch process of a solid Silicon wafer. The fabrication of the rotor follows a similar process, utilizing deposited oxide as a release layer. Using Silicon Dioxide and photoresist for masking, housing and rotor structures are etched from solid Silicon using timed Deep Reactive Ion Etching (DRIE). A unique feature of these processes is the self-masking of the spur gear in the housing and the shaft thru hole in the rotor during the second DRIE steps, which give the necessary multi-level, cross-sectional profile.