Background: Primary dysmenorrhoea (PDM) is inexorably common. PDM women suffer from cramping pain in the lower abdomen that starts with menstruation and lasts for 24-72 h. Up to 90% of adolescent girls and more than 50% of menstruating women worldwide report suffering from it. Ten to 20% of PDM women describe their suffering as severe and distressing. However, nothing is known regarding the association of PDM with possible brain anomalies or abnormalities. Methods: High-resolution T1-weighted anatomical brain magnetic resonance images (MRI) were acquired for each subject and inspected for incidental findings (normal variants and abnormalities) as a routine procedure in our PDM-related multimodal neuroimaging studies. Altogether, 330 right-handed young women [otherwise healthy PDMs = 163; non-PDM healthy controls (HCs) = 167] were enrolled during the period of 2006-2014. Binomial proportion test was performed for between-group comparisons. Results: PDMs demonstrated significantly higher prevalence of overall incidental brain MRI findings (PDMs: n = 18, 11.0%; HCs: n = 6, 3.6%; p = 0.005) that should be ascribed to a preponderance of normal variants (PDMs: n = 16, 9.8%; HCs: n = 3, 1.8%; p = 0.001), especially cavum septum pellucidum. No significant between-group difference of abnormal findings was found (PDMs: n = 2, 1.2%; HCs: n = 3, 1.8%; p = 0.336). Conclusions: We report here that otherwise healthy PDMs are associated with high prevalence of normal variants but not brain abnormalities. Our observations invite further epidemiological and neuroscientific studies.