Color vision deficiency has been associated with educational difficulties among male children, as well as attention-deficit hyperactivity disorder (ADHD). We examined the association of color vision deficiency with functional conditions, including ADHD, irritable bowel syndrome, enuresis and somatoform disorders, in a large population of male adolescents. We included all Israeli male adolescents that underwent medical and cognitive examinations during conscription between the years 2007 and 2013. The prevalence of ADHD, irritable bowel syndrome, enuresis, and somatoform disorders among color vision deficiency patients was compared to a control group. The study included 305 964 males aging 17 ± 0.6, of which 7584 (2.5%) had color vision deficiency. Using a multivariable analysis, the probability for irritable bowel syndrome, enuresis, and somatoform disorders among color vision deficiency patients was increased by 1.41, 1.94, and 3.87, respectively (P < .05). No significant association was found between ADHD and color vision deficiency. Color vision abnormalities are associated with functional disorders in male adolescents, including irritable bowel syndrome, enuresis, and somatoform disorders.