There are no data on the effects of fat-free mass (FFM) and body fat (BF) on prognosis in patients with myocardial infarction (MI). We investigated the effects of FFM and BF (which were estimated using formulas rather than direct measurements) on 30-day and long-term all-cause mortality in patients with MI who underwent percutaneous coronary intervention. We analyzed data from 6,453 patients with MI. The patients were divided into 2 categories (high/low) according to the fat-free mass index (FFMI) and 2 categories (low/high) according to the BF. The resultant 4 patient groups: HighFFMI-LowBF, HighFFMI-HighBF, LowFFMI-LowBF, and LowFFMI-HighBF, were compared. The lowest crude mortality after 30 days and in the long term was observed in the HighFFMI-LowBF group (3.0%,9.8%, respectively), followed by the HighFFMI-HighBF group (6.6%, 27.0%, respectively), the LowFFMI-LowBF group (10.4%, 36.0%, respectively), and the LowFFMI-HighBF group (14.7%, 56.8%, respectively). The difference was significant (p <0.0001), as was the difference between groups. After adjustment, the FFMI-BF groups independently predicted 30-day mortality (p = 0.003), but the risk was similar in all groups. Compared with the HighFFMI-LowBF group, the long-term mortality risk was similar in the HighFFMI-HighBF group (hazard ratio [HR] 1.11, 95% confidence interval [CI] 0.84 to 1.47, p = 0.47), but the LowFFMI-LowBF and LowFFMI-HighBF patients had a higher risk (HR 1.59, 95% CI 1.20 to 2.11, p = 0.001, HR 1.40, 95% CI 1.03 to 1.91, p = 0.033, respectively). Body composition predicted mortality better than body mass index in patients with MI. Mortality appeared to be inversely related to FFM, with patients with low FFM and low BF having a particularly high mortality risk. The body composition groups also confirmed the obesity paradox.