The aim of this paper is to find cellular automata (CA) rules that are used to describe S-boxes with good cryptographic properties and low implementation cost. Up to now, CA rules have been used in several ciphers to define an S-box, but in all those ciphers, the same CA rule is used. This CA rule is best known as the one defining the Keccak $\chi$ transformation. Since there exists no straightforward method for constructing CA rules that define S-boxes with good cryptographic/implementation properties, we use a special kind of heuristics for that – Genetic Programming (GP). Although it is not possible to theoretically prove the efficiency of such a method, our experimental results show that GP is able to find a large number of CA rules that define good S-boxes in a relatively easy way. We focus on the $4 \times 4$ and $5 \times 5$ sizes and we implement the S-boxes in hardware to examine implementation properties like latency, area, and power. Particularly interesting is the internal encoding of the solutions in the considered heuristics using combinatorial circuits; this makes it easy to approximate S-box implementation properties like latency and area a priori.