Malaise trap catches from representative lowland sites across the Neotropical Region are assessed for diversity of Diptera. Catches in all areas are numerically dominated by nematocerous groups (Cecidomyiidae, Sciaridae, Chironomidae, Ceratopogonidae), whereas the Phoridae belong to a middle group of families that are slightly less common. These catches are in great contrast to the level of effort of the taxonomic community dealing with these insects. Within the Phoridae, the diversity of two genera is compared between three sites: Barro Colorado Island, Panama; La Selva, Costa Rica; and Amacaycu, Colombia.