Management of HIV-infected and exposed children is challenging for health workers in primary care settings. Integrated management of childhood illness (IMCI) is a WHO/UNICEF strategy for improving morbidity and mortality in under 5 children attending first level facilities in developing countries. In high HIV-prevalence settings, IMCI includes an HIV component for identification and management of HIV-infected and exposed children, which requires health workers to ask all mothers about their HIV status and check all children for signs of HIV. Effective implementation of the HIV component depends on the ability and willingness of health workers to take every opportunity to identify HIV-infected children during routine care, and implementation in South Africa is poor. In 2006, we conducted 10 focus groups in two provinces in South Africa with IMCI-trained nurses, and with mothers attending first level facilities, to determine their attitudes towards, and experiences of, routine checks for HIV during consultations with sick children. Nurses were frequently unwilling to check for HIV in all children, believing it was unnecessary, unacceptable to mothers, and that they lack skills to implement HIV care. Nurses feared mothers would become upset or make a complaint. Mothers consistently recognised the importance of checking children for HIV and supported implementation of routine checks, although the attitude of the nurse was important in determining the acceptability of HIV-related questions. Mothers expressed fears about lack of confidentiality from nurses, and that receiving HIV-related services could lead to unintentional disclosure of their HIV status. Nurses lack the skills in HIV management and communication skills to implement the HIV component of IMCI. We identify issues relate to improved training, clear policies on record keeping, and organization of health services to respect privacy and confidentiality, to improve the willingness of health workers to provide HIV care and mothers to accept it.