Analysis of 202 medical histories of the Northern fleet naval pilots suggested the necessity to introduce the criteria of comorbidity number and formulation. It has been found that psychosomatic diseases (up to 60% of the cases) with the pathogenesis engendered by stress factor remain the leading cause for medical disqualification of Northern fleet naval pilots. The authors recommend changing over the nosologic diagnostics to physiological to optimize the aeromedical certification process. Probabilistic modeling of chronic pathology pathogenesis may be viewed as a foundation stone for programming as part of the pilots' anti-risk rehabilitation technology.