The executions of computer viruses are analyzed to develop register signatures for the viruses. The register signatures specify the sets of outputs the viruses produce when executed with a given set of inputs. A virus detection system (VDS) (400) holds a database (430) of the register signatures. The VDS (400) selects (710) a file that might contain a computer virus and identifies potential entry points in the file. The VDS (400) uses a virtual machine (422) having an initial state to emulate (714) a relatively small number of instructions at each entry point. While emulating each potential entry point, the VDS builds (716) a register table that tracks the state of a subset of the virtual registers (428). Once the VDS (400) reaches an emulation breakpoint, it analyzes the register table in view of the register signatures to determine whether the file contains a virus.