A method and system for protecting against side channel attacks on cryptographic systems that attempt to recover information from externally detectable signals, such as electromagnetic fields or power input variations. A system operates in accordance with the subject invention to process a message using a cryptographic protocol involving a secret key d. The protocol includes a step for computing the result of iteratively performing a binary operation [op] on a digital quantity G, where a secret key d is taken as an integer value, such as elliptic curve scalar point multiplication or modular exponentiation.