We aimed to study the prevalence patterns and course of benzodiazepine (BZD) abuse in an Israeli methadone maintenance (MMT) clinic using repeated random observed urine analysis as well as self-report data. Lifetime and current prevalence of BZD abuse were found in 66.3 and 50.8% patients, respectively. It was found that 44.6% of patients who abused BZDs during their first month of treatment ceased to do so after 1 year, while 27.4% who had not abused BZDs at the beginning of MMT did so after 1 year in treatment. Flunitrazepam was the most commonly abused BZD (92.9%), followed by diazepam (54.3%) and oxazepam (38.6%). Most of the patients swallowed BZDs (92.8%), 42.9% also smoked or snorted them while 8.6% injected BZDs intravenously. BZDs were used as self-medication for alleviating emotional problems rather than for recreational or other reasons. We conclude that BZD abuse is a significant clinical problem in heroin addicts both before entering and during MMT. MMT may have a positive as well as a negative influence on BZD abuse with the former being more prevalent.