The Reef Check survey methodology was designed for use by non-scientists to assess the health of coral reefs. The methodology focuses on the abundance of particular coral reef organisms that best reflect the condition of the ecosystem and that are easily recognisable to non-scientists. Selection of these “indicator” organisms was based on their economic and ecological value, their sensitivity to human impacts and ease of identification, allowing large numbers of non-scientists to participate in surveys. Indicators include a broad spectrum of fish, invertebrates and substrate categories that reflect human activities such as fishing, collection or pollution. The first global survey programme in 1997 provided scientific confirmation that coral reefs were facing a major crisis on a global scale. Since 2007, Reef Check Malaysia has conducted an annual Reef Check survey programme of Malaysia’s coral reefs. The paper presents an analysis of five years of data (2007-2011) collected from over 100 survey sites in both Peninsular and East Malaysia. Changing populations of fish and variations in live coral cover highlight local impacts on coral reefs, providing valuable information for managers and scientists. Data can be used to manage local threats to coral reefs, and contributes to building coral reef resilience.