Disclosed herein are systems and methods for parallel malware scanning in a cloud environment. In one exemplary aspect, a method may comprise identifying a plurality of agents connected to a server, wherein each agent is configured to synchronize data between a different computing device and the server. The method may comprise receiving, from a first agent of the plurality of agents, a request to scan the synchronized data for malware. In response to determining, from the plurality of agents, at least one other agent that comprises the synchronized data, the method may comprise partitioning the synchronized data into a plurality of portions. The method may comprise assigning a first portion for scanning to the first agent and at least one other portion for scanning to the at least one other agent, and aggregating scan results from the first agent and the at least one other agent.