The aim of the present work was to investigate CYP1B1 gene mutations in patients of Han Chinese ethnicity with primary congenital glaucoma (PCG), and explore the clinical characteristics associated with operative effects.Peripheral blood genomic DNA was extracted from patients with PCG to act as a PCR template. CYP1B1 mutations were identified from the amplified coding sequences of CYP1B1. A total of 238 patients, including 116 patients described previously, were used to examine the CYP1B1 mutation frequency. Of the 238 patients, 192 patients (306 eyes) who underwent first operative treatment from January 1991 to September 2007 in the Eye, Ear, Nose & Throat Hospital of Fudan University were analysed to investigate the relationship between clinical characteristics (including CYP1B1 mutation status) and surgical effect via statistical analyses (multivariate logistic regression and Cox regression).The frequency of CYP1B1 mutation carriers in Chinese patients with PCG is 17.2%, and nine novel CYP1B1 mutations were discovered. The median of onset age for patients with CYP1B1 mutations (2 months) is earlier than in patients without mutations (6 months). We identified that the mutant CYP1B1 gene, as well as poorer corneal transparency, was associated with better surgical outcome.Patients with CYP1B1 mutations tend to have a higher operative success rate in terms of better intraocular pressure control effect. The combination of the CYP1B1 genotype (with or without mutations) and preoperative corneal opacity score can partially predict the outcome of PCG surgery.