Retrocerebellar cysts of the brain represent the aspect that is important for determination of fitness for flight. The study was aimed to assess their impact on the pilot performance by conducting comparative analysis of MRI data of the first-year cadets and experienced pilots. We assessed the prevalence of retrocerebellar cysts among cadets and pilots, conducted non-contrast brain MRI, and compared the major academic and physical performance indicators, along with the results of professional psychological screen. The prevalence of retrocerebellar cysts among first-year cadets was 8.2%. High prevalence of asymptomatic retrocerebellar cysts among experienced pilots was revealed (two cases out of five). The intergroup comparison of indicators makes it possible to draw a conclusion about probable minor impact of such changes on fitness for flight. Further research is required to clarify the mechanisms underlying the impact of retrocerebellar cysts on the pilot performance and develop appropriate guidelines for medical boards.