Patients admitted in rehabilitation wards are usually older than those in general wards. Since elderly patients suffer from multiple co-morbidities thus showing a variety of symptoms, they are often at risk of polypharmacy. In the present retrospective observational study, we aimed to search for clinical characteristics of patients who were associated with factors influencing the number of drugs at discharge. One hundred and twenty-four patients (aged ≥65 years) who were admitted to rehabilitation wards in Setagaya Memorial Hospital between April and September either in 2013 and 2014 were enrolled in this study. Prescribed drugs during hospitalization, primary diseases and comorbid conditions were retrieved from the medical records of the patients. The mean age of the patients was 81 ± 8 years and 46% were men. Fifty-one patients (41%) were given polypharmacy at discharge. There was a significant reduction in the number of patients receiving non-steroidal anti-inflammatory drugs at discharge as compared admission. A multiple regression analysis revealed that the numbers of drugs prescribed at admission correlated (P < 0.05) with that prescribed at discharge. In addition, co-morbidities of heart disease and hypertension were associated with 1.2 and 0.9 more drugs at discharge, respectively. Pharmacists may intervene in the polypharmacy of patients more effectively if they take patients' clinical characteristics into account.