To investigate the incidence of and factors associated with persistent hypotony after trabeculectomy with mitomycin C in the Collaborative Bleb-Related Infection Incidence and Treatment Study (CBIITS), a 5-year prospective multicenter study. A total of 955 eyes of 955 patients who underwent trabeculectomy with mitomycin C were studied. Surgical failure was defined as insufficient intraocular pressure (IOP) reduction (IOP > 21 mmHg or < 20 % IOP reduction, or further glaucoma surgeries), loss of light perception, or persistent hypotony (IOP a parts per thousand currency sign 5 mmHg persisting for > 6 months). Factors associated with persistent hypotony in eyes with sufficient IOP reduction were determined by survival analysis and logistic regression analysis. The cumulative probabilities of surgical success and persistent hypotony at 5 years were 62.0 +/- A 1.7 % (+/- standard error) and 7.7 +/- A 0.9 %, respectively. In 685 eyes with sufficient IOP reduction, preoperative IOP (mmHg), limbus-based conjunctival flap, or choroidal detachment that occurred within 6 months of the surgery were significant risk factors for persistent hypotony [Cox proportional hazards regression model: hazard ratio, 0.95, 2.27, 3.24; 95 % confidence interval (CI), 0.91-0.98, 1.21-4.23, 1.51-6.95; P = 0.005, 0.01, 0.003, respectively]. Bleb infection and final visual acuity (logarithm of the minimal angle of resolution) were significantly associated with persistent hypotony (logistic regression: odds ratio, 8.74, 1.37; 95 % CI, 1.89-40.4, 1.03-1.82; P = 0.006, 0.029, respectively). In the CBIITS, eyes with successful IOP reduction, a limbus-based conjunctival flap, lower preoperative IOP, and choroidal detachment that occurred within 6 months of the surgery were identified as risk factors for persistent hypotony.