Functional genomics represents one of the most rapidly evolving fields of contemporary medical research. It is being more and more exploited in endocrinological research, as well, including studies on endocrine tumours. By comparing gene expression profiles of different tumour tissues or to their healthy counterparts, large amounts of information can be obtained that was unfeasible even until recently. There are only few data available on the pathogenesis of sporadic adrenal and pituitary tumours. Owing to recent studies applying functional genomics tools, novel genes were identified that could have pathogenetic relevance. Some of these genes may even be applicable in clinical practice, e.g. for the study of malignancy, determination of prognosis or the choice of therapy. In this short review, the authors attempt to present a synopsis of the possible applications of functional genomics in the field of endocrine tumours by summarizing recent studies on adrenal and pituitary tumours.