The need to accurately diagnose HIV-infected persons and monitor their immune status and sequelae from increased access to antiretroviral therapy dictated the establishment of a quality assurance (QA) system supported by dedicated personnel, financial resources, and a close monitoring system. Assessment of laboratories and personnel in Nigeria revealed the need for improved laboratory infrastructure and training, including on-site didactic and wet workshops and the institution of a tiered QA unit of laboratory regional officers, focal persons, and site monitors who provided guidance and continuous monitoring. Quarterly assessments and generated reports guided corrective actions. A sustainable quality laboratory system was developed for the first time in Nigeria with funding from the US President's Emergency Plan for AIDS Relief. With expansion from 7 to 34 comprehensive treatment sites, a tiered laboratory organizational structure with regional and site-based Nigerian quality control officers was developed. Measured improvements included reduction in deficiencies from 13% to 2%.