Background: SEA-ORCHID (South East Asia – Optimising Reproductive and Child Health in Developing Countries, www.seaorchid.org) is a five-year collaborative project between four countries in South East Asia and Australia. At nine hospitals in Thailand, Malaysia, the Philippines and Indonesia, SEA-ORCHID is investigating whether the health of mothers and babies can be improved by increasing the uptake of effective interventions; promoting evidence-based practice (EBP); enhancing access to reliable health information; and increasing the capacity for development of guidelines and systematic reviews. Methods: An important component of SEA-ORCHID has been a fellowships program in which clinicians and other professional staff from South East Asia spend one to two months at the three Australian SEA-ORCHID sites. The aim of the fellowships was to increase capacity for EBP and research synthesis by providing fellows with protected time and appropriate skills training. Fellows completed a pre-fellowship plan, learning portfolio and two post-fellowship evaluations. Results: There were 23 fellows between August 2006 and September 2007; seven were from Thailand, six from Malaysia and five each from the Philippines and Indonesia. The average fellowship lasted about five weeks (range 2 to 9). Fellows included eight obstetricians, six neonatalogists/paediatricians, five medical librarians, two labour room nurse-midwives, a neonatal nurse and a biostatistician. During the fellowships, fellows worked on Cochrane review protocols (11), designed training modules (8) including the RevMan 5 tutorial, and worked on clinical practice guidelines (4). Of the 11 Cochrane protocols, nine are in editorial review and one has been published in The Cochrane Library. The reviews being prepared by the Indonesian fellows comprise the first Cochrane activity in that country. Conclusions: Fellowships have been a valuable component of SEA-ORCHID and have helped to build capacity in research synthesis, especially Cochrane reviews. As SEA-ORCHID comes to a close, there is the challenge of finding ways of providing ongoing support for projects started during the fellowship. The success of the fellowships was due to planning, organisation, social and professional support and the commitment, hard work and perseverance of the fellows.