In a computer system, the integrity of lower layers is treated as axiomatic by higher layers. Under the presumption that the hardware comprising the machine (the lowest layer) is valid, integrity of a layer can be guaranteed if and only if: (1) the integrity of the lower layers is checked, and (2) transitions to higher layers occur only after integrity checks on them are complete. The resulting integrity "chain" inductively guarantees system integrity. When these conditions are not met, as they typically are not in the bootstrapping (initialization) of a computer system, no integrity guarantees can be made. Yet, these guarantees are increasingly important to diverse applications such as Internet commerce, intrusion detection systems, and "active networks." In this paper, we describe the AEGIS architecture for initializing a computer system. It validates integrity at each layer transition in the bootstrap process. AEGIS also includes a recovery process for integrity check failures, and we show how this results in robust systems. We discuss our prototype implementation for the IBM personal computer (PC) architecture, and show that the cost of such system protection is surprisingly small.