A programme for investigation of secondary amenorrhoea is described, which is based upon a functional classification of the endocrine causes of anovulation. All diagnostic enquiries not directly yielding a therapeutic dividend are excluded from this protocol. Three main categories of amenorrhoea are recognised: primary ovarian disease, hyperprolactinaemia and disorders of gonadotrophin secretion. There are subdivisions of each category, each with its own special diagnostic and therapeutic implications. Initial investigations take 6 weeks to complete and include measurements of follicle-stimulating hormone and prolactin, pituitary radiology and assessment of oestrogen production and of the response to clomiphene. The results of analysis of 75 consecutive cases of amenorrhoea and of 18 patients treated for infertility are presented and a cost benefit analysis applied.