CipherLinx® creates packets of data that consist of an intelligent preamble and address sent in the clear followed by a 40-bit counter, 8 data bits, and 80 integrity bits, for a total of 128 bits that are encrypted.

The enciphering function is based on the NSA-designed cipher Skipjack. Skipjack is a block cipher that has 80-bit keys and 64-bit data blocks. Since each packet is longer that 64 bits, Skipjack must be employed in an encryption mode. The particular encryption mode chosen for CipherLinx® is based on the CMC encryption mode, so that the resulting cipher is a special kind of function known as a "strong PRP" (sPRP). The encryption mode uses several invocations of Skipjack to encrypt the 128 bits in each data packet. The definition of these terms is quite involved, but more details can be found in ISE's evaluation report.

Another important factor in security is how the key is generated. When generating a cryptographic key from among all possibilities, it must be equally likely to choose any one of them. Each of the 80 bits of the key must be chosen uniformly (equally likely to be a '1' or a '0') and independently (the value of any bit does not depend on what value was chosen for any other bit). Keys are generated by the decoder through a series of activations of an input line on the decoder. A high-resolution timer in the decoder is triggered each time the input line is activated or deactivated. The low-order bits of this timer are used to create the key. This setup produces bits that are uniform and independent.