Objective: To investigate the association of area response rate with prevalence estimates of mental disorders in the 2nd World Mental Health Survey (WMHJ2). Methods: The sample of the WMHJ2 was selected from community residents in 129 areas from three regions of Japan. The surveys were conducted between 2013 and 2015, and 2450 (43.4%) responded. Mental disorders as well as three disorder classes (mood, anxiety, and substance use disorders) were identified using the WHO CIDI/DSM-IV. Response rates and 12-month and lifetime prevalences were calculated for each area. A generalized linear mixed model analysis was conducted to associate area response rate with the prevalence of mental disorders, controlling for sex, age, urbanity, and geographical region. Results: Area response rates ranged from 0.05 to 0.80 across the 129 areas. Area response rate was not significantly associated with 12-month or lifetime prevalence of mental disorder. Lifetime prevalences of substance use disorder were significantly lower in a survey with a higher response rate than a survey of the same area with a lower response rate. Conclusion: Response rate may not strongly affect the prevalence estimates of mental disorders in a community-based survey of the prevalence of common mental disorders during a particular time frame. However, a lower response rate could be associated with overestimation of lifetime prevalence of substance use disorder. This needs further elucidation.