Background: In the west, men are twice as likely as women to develop a drug problem, but female users have higher rates of morbidity than male users. Iran has the world highest per capita opiate consumption, but little is known about female drug users. In 2007, we established a free methadone clinic with ancillary services for female drug users in South Tehran. The aim was to explore the characteristics of female drug users seeking treatment for heroin dependence in Iran. Clients were interviewed about demographic characteristics, drug use and treatment history, and drug-related health problems. Urine and blood samples were collected and tested for morphine, HIV, hepatitis C virus (HCV), and sexually transmitted infections (STIs). Methods: Between August 2007 and October 2008, 78 women completed a baseline interview. The median age was 37 years, the main ethnic background was Persian (65%), and half of the clients were married. Opium and heroin and opium use was reported by 69% (n = 54) and 87% (n = 68) of clients, respectively. The mean duration of heroin use problems was 10.5 years, and only 20% of women reported ever having received drug treatment. HIV and HCV seroprevalence was 5% and 24%, respectively. Forty percent were sexually active when interviewed, and one third tested positive for an STI. Women had poor social functioning, high levels of depression, and poor general health. Results and Conclusions: Our clients were dependent users with a multitude of problems who had little or no contact with treatment agencies before this study. Many clients had made a transition from using opium to using heroin, and some had commenced injecting, placing them at risk for HIV and HCV infection. More women-only drug treatment services are needed to facilitate women's entry into drug treatment.