Transport related disadvantages, including unaffordable transport may lead to social exclusion and economic difficulties. In many cases, households choose to live in the city core and spend more on housing to lower their transport costs. Understanding how the affordability of transport is measured and distributed across cities is important to support the formulation of transport policies. This paper aims to examine the link between transport affordability and urban form by exploring household transport expenditures in twenty-two municipalities within Jakarta, Bandung, and Medan metropolitan areas in Indonesia. National household expenditure survey data are used to measure fuel, engine oil, minor repairs and maintenance, and public transport and other costs. In addition to the widely applied cost-toincome ratio method, this research proposes an alternative way to measure the affordability by using the data envelopment analysis (DEA) method. This method provides a more straightforward result that allows each municipality being observed to be ranked based on their affordability performance. The results suggest that transport affordability is affected not only by spatial structure and travel pattern, but also the choice and availability of transport modes. This research sheds new light on transport affordability in the developing cities context, and has implications for policy in the urban and transport sectors in Indonesia.