Skipjack is the encryption algorithm contained in the Clipper chip, and it was designed by the NSA. It uses an 80-bit key to encrypt 64-bit blocks of data. Skipjack can be more secure than DES, since it uses 80-bit keys and scrambles the data for 32 steps, or "rounds"; by contrast, DES uses 56-bit keys and scrambles the data for only 16 rounds.

The details of Skipjack are classified. The decision not to make the details of the algorithm publicly available has been widely criticized. Many people are suspicious that Skipjack is not secure, either due to oversight by its designers, or by the deliberate introduction of a secret trapdoor. By contrast, there have been many attempts to find weaknesses in DES over the years, since its details are public. These numerous attempts (and the fact that they have failed) have made people confident in the security of DES. Since Skipjack is not public, the same scrutiny cannot be applied towards it, and thus a corresponding level of confidence may not arise.