Urban health problems are very complex and affected by many factors, ranging from social and economic to environment and living conditions. In the middle of the 1980s, WHO introduced the Healthy Cities concept in Europe as a pilot project in response to a variety of urban problems including health issues. Then, in 1996 in Indonesia, the Ministry of Health and Home Affairs, began to develop Healthy Cities, including establishing a set of indicators to monitor improvements in urban health. However in 1986, ten years before the concept of Healthy Cities was formally recognised by WHO, the Indonesian State Ministry of Environment had developed Adipura – a clean cities program. The aims of both these programs are similar but they have a different history and were established by different departments. They also bring with them different policies, indicators and implementation methods. Both the Healthy Cities and Adipura programs operate without sufficient coordination to assess their effectiveness. Thus, they seem to be overlapping and competing, potentially leading to inefficient resource use. Based on an extensive literature review and document analysis, this paper compares and reviews the policies and existing indicators used by Healthy Cities and Adipura. This analysis has identified that the programs have similar goals in addressing urban problems, but have different agendas and performance indicators and different stakeholders involved in managing them. Therefore, strengthening the partnership between the key players involved in both approaches is an important strategy for improving the health and environmental conditions in Indonesian cities.