Harm reduction is fundamentally a movement intended to empower the patient and consumer of health services. This project applied harm reduction theory as a strategy to empower collaborating community partners and researchers to overcome their preconceptions about each other in order to create a successful HIV prevention intervention and evaluation study for injection drug using women. The Women's Options for Risk Reduction through Knowledge of Self (WORKS) intervention program offered a series of four HIV prevention workshops, in conjunction with sexually transmitted infection (STI) and HIV counseling and testing to female injection drug users (IDUs) or the partners of IDUs. This community collaboration was to integrate the strengths of researchers and service providers in a comprehensive approach to prevention evaluation. In this collaborative research context, capacity building meant developing the long-term goal, explicit commitment to and integration of evaluation into the overall operation of a HIV prevention service delivery organization. The WORKS Intervention collaboration's aim was to improve the capacity of community-based organizations (CBOs) to use research-based data on HIV risk taking behavior and prevention strategies to provide effective interventions and services and effectively evaluate their efforts. Barriers to successful planning, implementation, and evaluation are presented with the strategies used to overcome them. Intervention effectiveness results from the process evaluation are presented in the context of prevention and research capacity development in CBOs.