An unusual geological setting and a high level of endemism makes the Philippine islands of great interest to biogeography. These islands lie adjacent to the continental (Sunda) shelf, yet the majority of the islands have never been directly attached to the mainland. Existing hypotheses of colonization and diversification processes have been tested across multiple taxa, but only in ahistorical contexts. We present explicit phylogenetic predictions based on these hypotheses, and then test them using new molecular datasets for four Philippine birds. Two proposed colonization routes to the northern Philippines (from mainland Asia and Palawan) are difficult to differentiate from each other, except on the basis of outgroup, as are the two routes from the south (Sulu archipelago and Sulawesi). We find unique colonization and diversification patterns for each taxon. These results contrast with expectations from Pleistocene geography, with Luzon and Mindoro indistinguishable genetically, and Negros and Panay are often nonsister taxa. Combining these data with a literature search for studies addressing these patterns, Philippine organisms shows some evidence for each proposed colonization route but the greatest support is for the two routes from Borneo. Many taxa exhibit multiple colonization events using several of these routes, contrasting with past assumptions of single colonization events. Island-by-island differentiation within the Philippines follows, with patterns reflecting colonization patterns rather than Pleistocene geography, particularly for highland species. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 620–639.