Indonesia is located in one of the most seismically active regions in the world and often experiences damaging earthquakes. In the past the housing sector has sustained higher earthquake related damage and losses than other sectors. This is often attributed to the fact that the most common houses in Indonesia are non-engineered, built with poor quality workmanship, poor quality materials and without resilient seismic design features. However little effort has been made to quantify how fragile Indonesian houses are, or how their fragility may vary according to the population density or relative wealth of a region. It is not possible to derive empirical fragility functions for Indonesia due to insufficient damage data. The aim of this study is to determine whether existing earthquake fragility functions can be applied to common house types in Indonesia. Scenario damage analyses simulating the 2006 Yogyakarta and 2009 Padang events were undertaken several times testing different fragility functions. The simulated damage results were then compared to the damage observed post event to determine whether an accurate damage prediction could be achieved. It was found that the common house types in Yogyakarta and Central Java vary according to age of construction, location and relative wealth of a region and can be reasonably well represented by existing fragility functions. However, the houses in Padang and surrounding West Sumatra did not vary in a predictable manner and are more fragile than anticipated. Therefore, the fragility of the most common house types in Indonesia differs between Central Java and West Sumatra. This has important implications for seismic damage and risk assessment undertaken in Indonesia.