To determine the incidence of Chromosome 3 monosomy in iris melanoma using fine needle aspiration biopsy. Noncomparative case series of 17 patients. Fine needle aspiration biopsy was performed intraoperatively immediately before treatment of iris melanoma. Genetic analysis using DNA amplification and microsatellite assay was performed in the specimen. Clinical features and outcomes related to Chromosome 3 monosomy were reviewed. Disomy 3 was found in 5 melanomas (29%), partial Monosomy 3 in 7 melanomas (41%), and complete Monosomy 3 in 5 melanomas (29%). The only feature statistically associated with partial/complete Monosomy 3 (vs. Disomy 3) was older patients' age (median, 60 vs. 46 years, P = 0.03). A comparison of clinical features showed Monosomy 3 (vs. Disomy 3) tumors to be thinner (median, 2.8 vs. 4.2 mm) and with smaller base (median, 5.1 vs. 10 mm) but with greater iris seeding (mean, 5.7 vs. 2.4 clock hours) and greater angle seeding (mean, 3.2 vs. 0 clock hours), producing elevated intraocular pressure <22 mmHg (17 vs. 0%). Monosomy 3 tumors showed mixed/epithelioid cell type in 80% versus 0% in Disomy 3 (P = 0.14). No patients developed local melanoma recurrence or melanoma-related metastasis or death in the short 16-month mean follow-up. Using fine needle aspiration biopsy, cytogenetic analysis can be achieved in iris melanoma. Iris melanoma demonstrated partial or complete Monosomy 3 in 71%, and this statistically correlated with increasing patients' age. Mixed/epithelioid cell type was far more commonly seen in patients with Monosomy 3, although this did not reach statistical significance.