Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for affinity based ranking of native applications. In one aspect, a method includes accessing application affinity data for a user device from which a query was received, receiving a set of search results that each identify a respective resource determined to be responsive to the query, wherein one or more of the search results are a native application search results that each include a deep link to a respective one of the native applications installed on the user device from when the query was received, for each of the native application search results, determining the affinity score of the native application, adjusting the search results based on the affinity scores to generate an adjusted set of search results, and providing, to the user device, the adjusted search results.