We evaluated whether the presence of polycystic ovaries in adolescent girls as a cause of oligomenorrhoea and amenorrhoea would pose any protective effect against osteoporosis or low bone mineral density (BMD) compared with girls having similar menstrual dysfunction but normal ovaries. A cross-sectional observational study was done in consecutive girls, aged between 16 and 19 years, presenting to the adolescent gynaecology clinic with oligomenorrhoea or amenorrhoea. All patients underwent full hormonal profile assessment, pelvic ultrasound for ovarian morphology, bio-impedance estimation of body fat, and dual-energy X-ray absorptiometry and quantitative peripheral computed tomography scans to determine BMD in axial and appendicular skeletal sites. Polycystic ovaries were diagnosed according to ultrasound morphology. These were then compared with an age-matched eumenorrhoeic control group that had undergone the same evaluation. Of 45 patients with oligomenorrhoea or amenorrhoea, 14 (31%) were diagnosed to have polycystic ovaries, while the other 31 had normal ovaries. The control group consisted of 45 age-matched eumenorrhoeic girls. The group with normal ovaries had lower BMD at the lumbar spine and hip, as well as lower total tibial volumetric BMD, than the eumenorrhoeic controls, but there were no significant differences between the group with polycystic ovaries and eumenorrhoeic controls. We conclude that adolescents with oligomenorrhoea and amenorrhoea with normal ovaries had lower BMD than eumenorrhoeic ones, but those with polycystic ovaries had BMD values comparable to those of eumenorrhoeic controls despite their menstrual dysfunction.