BACKGROUND: The North-east Indian states of Manipur and Nagaland consistently report relatively high HIV prevalence. The targeted HIV prevention interventions in these two states are mostly delivered by non-government organizations (NGOs), and prevention of HIV transmission by injecting drug use is their main focus. Most injecting drug users (IDUs) are male, and the services are primarily tailored to meet their needs, which are not necessarily the same as those for women. This qualitative study describes the health service needs of women who use drugs and alcohol in Manipur and Nagaland, with the goal of identifying strategies and activities that can be implemented by NGOs wanting to improve their reach among vulnerable women. METHODS: In 2009-10, semi-structured in-depth interviews were conducted with 27 key informants and nine focus group discussions (FGDs) with women who use drugs and alcohol, and two FGDs with male IDUs. The thematic areas covered included: the context of female drug and alcohol use; drug and alcohol use patterns; HIV risk behaviours; barriers and facilitators of service use; perceived health needs; and expressed health service needs. The data were recorded, transcribed, translated and thematically analysed. RESULTS: The most problematic substance for women from Nagaland was alcohol, and for women from Manipur it was heroin. The most commonly identified health problems were primarily related to the women's drug and alcohol use, reproductive health and mental health. Other problems of major concern included social exclusion, violence, children's welfare, and financial difficulties. The expressed service needs of these women were women-only integrated health services, women-only detoxification and rehabilitation services, mental health services, desensitization of mainstream health workers, free access to medicines, assistance to meet basic needs, and a safe place for engaging in sex work. CONCLUSION: The expressed health and other service needs of women who use drugs and alcohol in Manipur and Nagaland do not match the services currently provided by HIV prevention NGOs, and this may, in part, account for the relatively poor uptake of these services by women. Strategies and activities that can be implemented by NGOs to strengthen their reach to vulnerable women are identified. However, many of these women's needs are beyond the scope of services typically offered by HIV prevention NGOs, and require a coordinated multi-sectoral response.