Venous thromboembolic complications—deep vein thrombosis and pulmonary embolism—occur in a significant proportion of hospitalized medical patients. The incidence in acutely ill medical patients is 10%-40%, equivalent to that seen in general surgical patients. Prophylaxis is effective and well tolerated, yet remains under-prescribed in medical wards. Current recommendations for prophylaxis are generalized and do not specifically address many patient groups. Data on the prevalence in patients with chronic obstructive pulmonary disease, heart failure, and infectious diseases are limited. However, studies on large numbers of hospitalized patients with these admission diagnoses have provided important information on incidence, and the efficacy of thromboprophylaxis. This review summarizes current knowledge of the epidemiology of venous thromboembolism in patients with chronic obstructive pulmonary disease, heart failure, and infectious diseases, and highlights the benefits of, and needs for, appropriate prophylaxis in these groups. Increased awareness of the prevalence of thrombosis in the major subgroups of medical inpatients should improve the prescribing of prophylaxis and prevent potentially avoidable and costly complications.