Phenotypic analysis combined with molecular genetics is a powerful tool for mapping gene function onto the genome. Phenotypic data are, by their nature, descriptive, and as varied as the range of mutant phenotypes that can be presented by the organism under study. This paper discusses the mechanisms FlyBase has implemented to systematise published phenotypic data about Drosophila, and provides an introduction to the query tools available for the mining of the data. Though FlyBase is specific to Drosophila, the issues faced in devising protocols for capturing, storing and reporting data are the same issues faced by any database with an interest in using phenotypic data to maximise the potential of genomic analysis.