Background Genitourinary prolapse is a common problem, the pathophysiology of which is unknown. Methods We analysed vaginal-epithelial tissue from premenopausal women with genitourinary prolapse and compared them with controls. Findings We found that genitourinary prolapse is associated with a reduction in total collagen content and a decrease in collagen solubility. Both intermediate intermolecular cross-links and advanced glycation cross-links were increased in prolapse tissue. Collagen turnover, as indicated by matrix metalloproteinase activity, was up to four times higher in prolapse tissue. Collagen-type ratios, mature cross-link pyridinoline and total elastin content were similar in both prolapse and control tissues. Increased collagenolytic activity causes loss of collagen from prolapse tissue. Interpretation Based on these findings, we have identified a probable mechanism for genitourinary prolapse. Development of agents to inhibit collagenolytic activity may help in the treatment of this condition.