This article reflects on the challenges of strengthening health research capacity from within Samoa. It examines the status of health research and related curricula in Samoa and discusses the outcomes of a new postgraduate applied social and health research methods course taught in Samoa for the first time from 5 January to 12 February 2010 by the Department of Preventive and Social Medicine, University of Otago in collaboration with the Centre for Samoan Studies, National University of Samoa. The article argues that collaborative health research courses such as this methods paper can fill a curriculum gap in New Zealand and Samoa and contribute directly toward strengthening Samoa health research capacity in ways that benefit both Samoa and New Zealand. This initiative can be a flagship for strategies operating from within Samoa that can build real win-win type partnerships. These can be ably led by Samoans for the ultimate development of an affordable and sustainable quality health and education infrastructure for Samoa.