As genomic studies accrue in reproductive medicine, the value of accurate phenotyping to match precise genotyping will increase. This combination is essential for the proper interpretation of “function” in functional genomics. This review outlines ways in which components of the standard clinical evaluation of male infertility, including the history, physical examination, semen analysis and testis biopsy, can be improved to increase phenotypic information and how that information can be used to facilitate scientific discovery.