Malnutrition is highly prevalent among hospitalized patients; thus, an accurate identification of malnutrition could improve the outcome of these patients. The aim of the present paper was to apply multiple methods to evaluate the prevalence of malnutrition and clinical correlates in patients admitted to in-hospital cardiac rehabilitation. We performed a prospective study of 426 patients admitted to in-hospital cardiac rehabilitation: 282 (66.2%) had undergone a major cardiac surgery and 144 (34.8%) had experienced heart failure. The albumin level and Mini Nutritional Assessment (MNA) scores were applied to evaluate the nutritional status of these patients. Serum albumin levels were < 3.5 g/dl in 147 (34.5%) patients, and MNA scores were < 24 in 179 (42.0%) patients. Patients with malnutrition or a risk of malnutrition had lower haemoglobin values, lower EuroQol scores and poorer functional status. Female gender, age, functional status and Cumulative Illness Rating Scale severity were predictors of malnutrition. Over a median follow-up of 47 months, MNA scores <24 were associated with higher mortality, even after correction for confounding variables. In conclusion, in patients admitted to in-hospital cardiac rehabilitation, malnutrition and risk of malnutrition frequently occur and are associated with poor functional status, higher clinical complication rates and long-term mortality.