The execution of anti-virus programs can be accelerated in a virtual desktop environment. In one embodiment, a server hosts a plurality of virtual machines. Before performing a virus scan on a file, the server computes a signature value of the file, compares the signature value with the stored signature values in a central database, and performs virus scan on the file according to the result of the comparison. If the signature value exists in the central database, the virus scan on the file can be skipped.