The NeuroHomology database is a knowledge-based database that contains related sets of data on brain structures, connections and homologies in different species. In this paper we propose a set of rules, embedded in the database, for evaluation of the similarity between brain structures and of the neuroanatomical connections as reflected in the literature. The NeuroHomology database is a tool for search of neurobiological information and an expert system for evaluation of the similarity between brain structures in different species. This can be useful for computational neuroscientists when data about putative homologous structures is used in computational models of brain structures.