PURPOSE: To evaluate the prognostication of choroidal melanoma (CM) by the gene expression profiling (GEP) test. DESIGN: Cohort study. METHODS: Retrospective review of 293 CM patients from 2 centers. RESULTS: Of 293 patients, 132 (45%) were class 1A by GEP, 63 (22%) were class 1B, and 98 (33%) were class 2. Class 2 tumors had more ciliary body involvement and greater largest basal dimension (LBD), and were thicker. GEP results and increasing LBD were independently predictive of time to metastasis. Kaplan-Meier survival analysis estimated the probability of 3-year metastasis-free survival (MFS) of 0.99 in class 1A, 0.90 in class 1B, and 0.60 in class 2. The probability of 3-year MFS was 0.49 in class 2 patients with LBD ≥ 12 mm vs 1.00 in those with LBD < 12 mm, 0.89 in class 1B with LBD ≥ 12 mm vs 0.93 in those with LBD < 12 mm, and 0.99 in class 1A with LBD ≥ 12 mm vs 1.00 in those with LBD < 12 mm. In American Joint Committee on Cancer (AJCC) stage I CMs, the probability of 3-year MFS was 1.0 for class 1A and 1B, and 0.79 for class 2. In stage II CMs, the probability of 3-year MFS was 0.99 for class 1A, 0.89 for class 1B, and 0.61 for class 2. In stage III CM, the probability of 3-year MFS was 1.0 for class 1A, 0.60 for class 1B, and 0.41 for class 2. CONCLUSIONS: GEP testing provided significant prognostic information for CM. Class 2 tumors with LBD ≥ 12 mm and class 2 and 1B tumors with AJCC stage III showed significantly worse prognosis.