The increasing ascendancy of 'gender mainstreaming' as the central approach to improving gender equity has largely determined strategies to integrate a gender focus in sector-wide approaches (SWAps). This paper explores the impetus for and process of gender mainstreaming in SWAps in the Ministries of Health in Uganda, Ghana, Malawi and Mozambique, and outlines some achievements and challenges. The shifting and contested relationships between the Ministry of Health, donors and other government ministries (such as Ministries of Finance and Ministries of Women's Affairs/Gender) are important in shaping the opportunities and constraints faced in gender mainstreaming. The refocusing of resource allocation to different sectors has led to changes in the balance of power between the various actors at the national level, with diverse implications for promoting gender equity in health. Some of the achievements to date and ongoing challenges are explored through concrete examples from different countries. These include: the development of structures for mainstreaming, including the dilemmas of the 'focal points' approach and the role of national gender mainstreaming machinery; the need for training and building capacity to identify and address gender issues, which involves engaging with new languages and concepts, and developing new skills; building alliances, consensus and momentum; integrating gender concerns into policy and planning documents; and promoting gender equity in human resources in the health sector. Cross-cutting themes underlying these challenges are the need for gender-specific information and ways to finance mainstreaming strategies. Implications are drawn for ways forward, without losing sight of the challenge of translating discourses of gender mainstreaming, and its central ideal of social transformation, into pragmatic strategies in the bureaucratic environment.