Parasitic infections still remain a major health threat in developing countries. Herein we report a systematic characterization of the structure–activity relationships (SAR) of a comprehensive set of benzimidazole derivatives tested against Trichomonas vaginalis and Giardia intestinalis. The analysis was based on pairwise comparisons of the activity similarity and molecular similarity using different molecular representations. Overall, results encourage simultaneous lead optimization efforts for benzimidazole derivatives active against both protozoan. In order to explore the activity profile of the benzimidazoles against the two parasites, we developed the dual activity-difference (DAD) map. DAD map is a complementary approach to systematically characterize the SAR of compound data sets.