People with mental disorders are susceptible to physical comorbidities. Mind-body interventions are important for improving health outcomes. We examined the prevalence of physical comorbidities and their differences by diagnoses and sex among psychiatric inpatients. The dataset, from National Health Insurance claims data, included 48,902 adult inpatients admitted to psychiatric wards for at least 2 days in 2016 treated for schizophrenia, schizotypal and delusional disorders, or mood disorders. We identified 26 physical comorbidities using the Elixhauser comorbidity measure. Among schizophrenia-related disorders, other neurological disorders were most common, then liver disease and chronic pulmonary disease. Among mood disorders, liver disease was most common, then uncomplicated hypertension and chronic pulmonary disease. Most comorbid physical diseases (except other neurological disorders) were more prevalent in mood disorders than schizophrenia-related disorders. Male and female patients with schizophrenia-related disorders showed similar comorbidity prevalence patterns by sex. Among patients with mood disorders, liver disease was most prevalent in males and third-most in females. In both diagnostic groups, liver disease and uncomplicated diabetes mellitus were more prevalent in males, and hypothyroidism in females. Mental health professionals should refer to a specialist to manage physical diseases via early assessments and optimal interventions for physical comorbidities in psychiatric patients.