Tropical secondary forests are increasingly widespread, but their potential for conserving endemic birds remains unclear. Previous studies report different results; however all have been restricted to geographically discreet locations. This is important as different ecosystems are influenced by different external factors, possibly influencing conservation potential. Here we use consistent survey methods to examine how endemic bird richness varies between primary and secondary forest habitats in two widely separated tropical ecosystems, providing a more global context for evaluating the conservation value of secondary forests. Research was completed in Lambusango Forest Reserve (LFR) on Buton Island, Sulawesi, and Cusuco National Park (CNP), a Honduran cloud forest reserve. Bird communities in both forests were surveyed using 50 m radius point counts. Vulnerability assessments based on ecological theory on avifaunal assemblages were then conducted, which suggested endemics in LFR to be more susceptible to disturbance than those in CNP. Contrary to the results from our vulnerability assessments, endemics in CNP were less tolerant of moderate habitat modification than those in LFR. Richness of Mesoamerican endemics per study site declined significantly between core zone forest (6.34 ± 0.81) and more degraded forest in the boundary zone (3.86 ± 0.69). Richness of Wallacean endemics was similar in primary (4.89 ± 1.68) and disturbed secondary forest (4.52 ± 1.62). We recommend considering local and regional biogeographical and ecological factors when determining the conservation value of secondary forests, and suggest examples of potential importance, including differential community richness, influence of figs and human settlement patterns.