Funds to developing countries for HIV/AIDS programmes have noticeably increased. For civil society organisations (CSOs), one challenge of project implementation is the difficulty in assessing their interventions. A qualitative study was conducted in Malaysia and the Philippines with CSOs to identify the obstacles to HIV project evaluation. Twenty-five bodies—CSOs, donors, governments and the United Nations—in both countries were interviewed. The findings show that despite contrasting political and socio-economic contexts, both countries' CSOs share similar impediments to evaluation, including the lack of evaluation expertise, inadequate resources, onerous reporting obligations and constraints in evaluating interventions with marginalised groups. Copyright © 2013 John Wiley & Sons, Ltd.