Systems and methods utilizing the network layer and/or application layer to provide security in distributed computing systems in order to thwart denial of service attacks. The systems and methods of the present invention utilize puzzles placed at the network layer level and/or application layer level to protect against denial of service attacks. Further, the systems and methods of the present invention advantageously provide a robust and flexible solution to support puzzle issuance at arbitrary points in the network, including end hosts, firewalls, and routers and thereby a defense against denial of service attacks.