This article attempts to provide an understanding to what extent institutional change of the functional activities of microfinance influences some specific health-related outcomes for the ultra-poor people in Bangladesh. It examines impact of the ‘Challenging the Frontiers of Poverty Reduction-Targeting the Ultra Poor’ (CFPR-TUP) programme on health-related outcomes using a large balanced panel data set (2002, 2005 and 2008) from rural areas of Bangladesh. The main objective of this article is to examine both short- and long-term impacts on health-related issues of the ultra poor using both conditional and unconditional difference-in-differences (DID). In particular, this article examines the distinction between treatment and control groups in base year and the year followed up as well as the impact on coping ability. This study finds the significant impact of the programme on investment in health and awareness indicator such as usage of sanitation though we are suspicious about its sustainability. The programme therefore has sustainable impact on health investment and to some extent, on coping ability.