Introduction and hypothesis Women with hereditary disorders of connective tissue (HDCT) are at increased risk of pelvic organ prolapse (POP) and stress urinary incontinence (SUI). We hypothesized that patients would have increased incidence and severity of perioperative complications up to 6 weeks after surgeries for POP/SUI. Secondary objectives were to compare pre- and post-operative pelvic floor symptoms and anatomical support as well as pelvic floor disorder recurrence. Methods In this multi-center retrospective cohort study, we identified patients with HDCTs by patient history and ICD-9 codes over an 11-year period. Controls without HDCTs were matched 2:1 to the primary POP or SUI procedure and surgeon. Demographic characteristics, perioperative pelvic floor information and complications were collected. A sample size of 65 HDCT patients and 130 controls was calculated to detect a 20% difference in complications with 80% power and alpha of 0.05. Results We identified 59 HDCT patients and 118 controls. Of the women with HDCTs, 49% had Ehlers–Danlos, 22% joint hypermobility syndrome, 15% Marfan syndrome, and 14% had others. Compared with controls, HDCT patients had more total perioperative complications (46% vs 22%, p =  0.002); an age-adjusted relative risk of complications was 1.4 (CI 0.7–2.6). HDCT patients had more Clavien–Dindo grades I and II complications ( p =  0.02, 0.03) and more hospital readmissions (14% vs 3%, p =  0.01) than controls. There was no difference in the incidence of specific complications nor was there a difference in recurrence of POP (10%) or SUI (11%) between groups. Conclusions Patients with HDCTs had more Clavien–Dindo grade I and II complications following pelvic floor reconstructive surgery and more readmissions.