Anthropogenic habitat changes and the introduction of pigs, dogs, cats and rats have caused a catastrophic decline in the terrestrial biodiversity of Pacific archipelagos. At present, economic globalization and an increased demand for timber are promoting industrial logging and plantation expansion. Commercial logging can be sustainable but in practice it more often leads to land degradation, especially on small flat islands. On large and mountainous islands, however, more modest impacts can be expected as the narrowly endemic species tend to inhabit montane forests where logging is difficult. In this study we use ornithological data collected at different elevations to assess the extent to which the avifauna of Makira, a large mountainous island in Melanesia, will be affected by deforestation of the lowlands, most of which are under timber concessions. Our data suggest that a majority of the endemic bird species use lowland forest to some extent and that this may even apply to species hitherto associated with montane forest. If current commercial forestry programmes are continued, the forest habitat may be disturbed or lost over large parts of Makira, potentially undermining the natural resource base for the local subsistence economy, exacerbating climate change and threatening the integrity of one of the most important areas for biodiversity conservation on earth. Our study highlights the importance of understanding the habitat requirements of endemic species and the urgency of establishing and effectively managing community-based protected areas in suitable lowland forests of the Pacific.