We surveyed birds during May and June, 2001–2003, on 26 islands and 1 mainland location in Boston Harbor, MA. We detected 136 species, 67 of which were suspected of breeding. Abundant breeding seabirds included Double-crested Cormorants (Phalacrocorax auritus), Herring Gulls (Larus argentatus), and Great Black-backed Gulls (Larus marinus). We found 73 Common Eider (Somateria mollissima) nests on Calf, Green, Middle Brewster, and Outer Brewster Islands in 2003, making Boston Harbor one of the largest, southernmost nesting areas for this species on the western Atlantic Ocean. We surveyed 7 wading bird colonies composed of Black-crowned Night-Heron (Nycticorax nycticorax), Great Egret (Ardea alba), Snowy Egret (Egretta thula), Glossy Ibis (Plegadis falcinellus), and Little Blue Heron (Egretta caerulea). We found a colony of Least Terns (Sterna antillarum), a state-listed species, on Rainsford Island. We estimated that 49 species of landbirds nested on Boston Harbor islands, but most islands had few species (mean = 9.8 [± 2.2 (SE)] species per island), presumably because many islands were small and dominated by non-native second-growth forests. The most widespread species were Yellow Warbler (Dendroica petechia), Song Sparrow (Melospiza melodia), and Red-winged Blackbird (Agelaius phoeniceus). We also detected over 50 species of migratory birds which did not nest on islands in the Harbor, including many species of shorebirds and warblers.