Report of a two-day meeting, organised by the World Health Organisation and the Joint United Nations Programme on HIV/AIDS (UNAIDS) on 1-2 June, 2009 in Nairobi, brought together 33 scientists and public health experts from 11 countries (including eight countries in sub-Saharan Africa) to discuss operations research on male circumcision for HIV prevention, and to set priorities for the next two years. Considerable progress had been made since the first meeting on MC operations research in June 2007.