Blood-oxygenation-level-dependent functional magnetic resonance imaging is a noninvasive technique that has become increasingly popular in the neurosciences. It measures the proportion of oxygenated haemoglobin in specific areas of the brain, mirroring blood flow and therefore function. Here we review how the findings from functional studies impact on areas of gynaecological practice as diverse as chronic pain, continence, and premenstrual dysphoric disorder. Finally we review some of the more novel applications of the technique, such as imaging of pelvic floor function and the effects of hypoxia on the fetus.