Numerous countries have witnessed increasing misuse of benzodiazepines. This cross-sectional study assessed the factors associated with prescription of benzodiazepines for users of the Municipal Health Service in Colonel Fabriciano, Minas Gerais State, Brazil. Data were collected from official records on drug prescription (n = 1,866) from September to October 2006. Bivariate and multivariate analyses using Poisson regression were performed. Prolonged benzodiazepine use was independently associated with benzodiazepine type and patient participation in health programs. Concomitant use of other psychoactive drugs was independently associated with age and participation in health programs. Type of benzodiazepine (clonazepam or diazepam) was independently associated with age and gender, as well as with participation in health programs. Factors associated with benzodiazepine prescription show the problem's extent and should be considered in planning interventions to rationalize the use of these drugs in Brazil, particularly through health program planning.