A new adaptor protein complex, termed AP-3, has recently been identified in mammalian cells, and genetic studies in yeast have revealed a functional role for the AP-3 complex in cargo-selective transport via a new alternative trafficking pathway from the Golgi to the vacuole/lysosome. Here, the authors review what is currently known about the AP-3 complex and discuss recent insight into its function in multicellular organisms that has come from the finding that mutations in AP-3 subunits correspond to classical mutations in Drosophila and mice.