1. Sophisticated and sensitive technologies now allow separation, quantification and chemical characterization of numerous compounds that play roles in chemical communication, chemical defence and aggression, in interactions between conspecific or heterospecific individuals. In the particular subfield of mammalian chemical communication, these rapid technological advances, combined with a frequent lack of technical background, have led to important errors in both chemical characterization of molecules and interpretation of their roles as chemical mediators of communication. 2. The aim of this article is to highlight some of these methodological and analytical pitfalls and to provide a basis for better understanding of chemical mediation of communication in mammals. We compiled the recent literature treating molecules found in mammalian secretions and having putative roles in communication. A selection of 41 published studies dealing with 33 mammal species revealed reports of 857 different molecules. Based on the five main metabolic pathways responsible for the biosynthesis of most known secondary metabolites, we propose nine general biochemical rules that will help researchers to avoid errors of chemical characterization and to aid in interpreting the possible functional role of identified molecules as chemical mediators of mammal communication. 3. Following these nine rules, we show that published studies include reports of molecules that are incorrectly or ambiguously named, molecules of exclusively non-natural origin, molecules produced by other organisms but not directly by mammals, and molecules of biological origin and possibly produced by mammals. Only the last two of these classes could conceivably play roles as mediators of mammalian communication. We discuss the potential roles of these compounds as reported in the publications we reviewed. 4. Our recommendations concerning technical, analytical and statistical aspects of the identification of compounds and interpretation of their roles should help chemical ecologists ask the appropriate questions about the accuracy of their identifications of molecules, the biological relevance of molecules they do identify and the possible functional roles of these molecules in mammalian communication.