Background Patients with comorbidities are becoming more and more common in Italian rehabilitative wards. These comorbidities are considered a major problem for inpatient rehabilitation, due to the fact that they cause longer lengths of stay, higher costs, and lower functional results. Methods To investigate the possible relationships between comorbidity, functional impairment, age, and type of discharge in patients hospitalized in postacute rehabilitation facilities, we planned an observational study. A total of 178 consecutive inpatients (average age: 78 years [range: 39–99]) from postacute rehabilitation facilities were recruited. Primary diagnosis, comorbidity rating (Cumulative Illness Rating Scale – Geriatric version, CIRS-G) and functional impairment score (Functional Independence Measure, FIM™) were evaluated at admission. The FIM™ rating was also assessed at hospital discharge. Results A total of 178 of the 199 enrolled patients completed the rehabilitation treatment (89.4%). The average length of stay was 46 ± 24 days. CIRS-G showed an average comorbidity score for each patient of 4.45 ± 1.69. The average FIM™ rating was 79 ± 24.88 at admission, and 91.9 ± 25.7 at discharge. Diagnosis at admission (grouped according to the International Classification of Diseases 9-CM) seemed to correlate with functional results, since lower rehabilitative efficiency was obtained for patients who had a history of stroke. Conclusion The number and type of comorbidities (CIRS-G) in rehabilitation inpatients do not seem to affect functional outcomes of treatment. The determining factor for a lower level of functional recovery seems to be the diagnosis at admission.