To evaluate the risk factors for secondary membrane (SM) formation after congenital cataract surgery with intraocular lens (IOL) implantation. A retrospective non-interventional comparative study. Thirty-nine patients (63 eyes) aged 1-135 months. The study included patients who underwent cataract extraction and primary IOL implantation between 1994 and 2001 at the University Hospital. The postoperative follow-up was 6-24 months. Thirty-three eyes received a poly(methyl methacrylate) (PMMA) IOL without square edges, 29 eyes received a hydrophobic acrylic IOL with truncated square edges (AcrySof), and there was no data for IOL type in one eye. Thirty-nine eyes had primary posterior capsulotomy (PPC) and anterior vitrectomy (AV) and in 24 eyes the posterior capsule was left intact. Cox proportional hazard regression analysis was performed to identify significant risk factors for SM formation, and Wilcoxon test to evaluate the difference in time from surgery to SM formation. SM developed in 24 eyes (38 %)--58 % of eyes with an intact posterior capsule and 26 % of eyes having PPC and AV, 42 % of eyes with a PMMA IOL, and 34 % of eyes with an AcrySof lens. In multivariate Cox regression analysis intraoperative PPC and AV (P = 0.02) and AcrySof lens implantation (P = 0.097) were associated with decreased postoperative incidence of SM formation. Median time until SM development was 2.9 months with PMMA IOLs (range 1-17 months) and 6 months with AcrySof lenses (range 1-21.8 months) (P = 0.037). Posterior capsule management as well as IOL design and material influence the incidence and the timing of SM formation after primary IOL implantation in children.