Hurricanes and other tropical cyclones have devastating effects on society. Previous case studies have quantified their impact on some health outcomes for particular tropical cyclones, but a comprehensive assessment over longer periods is currently missing. Here, we used data on 70 million Medicare hospitalizations and tropical cyclone exposures over 16 years (1999–2014). We formulated a conditional quasi-Poisson model to examine how tropical cyclone exposure (days greater than Beaufort scale gale-force wind speed; ≥34 knots) affect hospitalizations for 13 mutually-exclusive, clinically-meaningful causes. We found that tropical cyclone exposure was associated with average increases in hospitalizations from several causes over the week following exposure, including respiratory diseases (14.2%; 95% confidence interval [CI]: 10.9–17.9%); infectious and parasitic diseases (4.3%; 95%CI: 1.2–8.1%); and injuries (8.7%; 95%CI: 6.0–11.8%). Average decadal tropical cyclone exposure in all impacted counties would be associated with an estimated 16,772 (95%CI: 8,265–25,278) additional hospitalizations. Our findings demonstrate the need for targeted preparedness strategies for hospital personnel before, during, and after tropical cyclones.