Stephen Franks has both clinic and laboratory-based programmes of research in the field of normal and disordered function of the hypothalamic-pituitary-ovarian axis. He has a major interest in polycystic ovary syndrome (PCOS), which is not only the commonest cause of anovulatory infertility but is also a major risk factor for development of type 2 diabetes. His research includes investigation of disorders of ovarian follicle development, the mechanism(s) of anovulation, and of the characteristic metabolic abnormalities; it focuses particularly on the interaction between genetic and environmental factors in the aetiology of the syndrome. .

His earlier studies in the field of PCOS have included work elucidating the wide prevalence and spectrum of presentation of the syndrome, which led to revision of the diagnostic criteria for PCOS. His team also described a disorder of energy balance (associated with insulin resistance) in women with PCOS and demonstrated that metabolic abnormalities in PCOS are linked to menstrual dysfunction. They were amongst the first to promote low-dose gonadotropin regimens for the safe treatment of infertility in women with PCOS, a procedure that has now been adopted worldwide. In laboratory-based studies his team found evidence for an intrinsic ovarian abnormality of steroidogenesis in PCO ovaries. Another important aspect of the work on PCOS (in collaboration with, first, Bob Williamson, later Mark McCarthy and, more recently, Cecilia Lindgren), has been the search for the genetic basis of PCOS. He is currently a member of the Steering Committee for the international consortium studying the genetics of PCOS which has recently published a large genome-wide association study (GWAS) identifying key susceptibility loci for PCOS. Together with Professor Kate Hardy, he described abnormalities in early follicular development in the polycystic ovary, and this team has shown that this phenomenon is associated with abnormal expression of growth factors implicated in follicle development.