Benzodiazepines are useful and effective psychotropic agents used worldwide. However, the long term use of the drugs can lead to serious adverse health effects such as psychomotor and cognitive impairment, especially in the elderly. In Japan, there are very few reports concerning long-term use of benzodiazepines, and no countermeasures have been instituted. Thus, this study assessed the characteristics of long-term prescription of benzodiazepines at a university hospital in Japan. A cross-sectional study using the database of a computer ordering system examined 4,239 adult outpatients who were prescribed benzodiazepines at a university teaching hospital between July 2002 and June 2003. The patients were divided into two groups: those with long-term (≥ 3 months) and short-term (≤ 2 months) prescriptions. A logistic regression model was used to analyze the effect of patient age on long-term benzodiazepine prescription. Adjusting for patient gender, pharmacological half-life of the drug, and department group, a logistic regression model showed that long-term benzodiazepine prescription occurred more frequently in older patients (p < 0.0001 in trend tests) and varied according to the physician's specialty (p < 0.0001). Benzodiazepines were more frequently prescribed for long term in the elderly by internal medicine group (p = 0.003). Of the patients older than 71 years (n = 1,105), 86% were assigned to the long-term group and were more likely to have been prescribed benzodiazepines by an internist than a surgeon (p < 0.0001). The appropriate prescription of benzodiazepines in the elderly should be included in the educational programs at teaching hospitals, and rational prescribing needs to be monitored carefully.