We identified natural pits associated with avian mortality at the base of Kiska Volcano in the western Aleutian Islands, Alaska in 2007. Living, moribund, and dead birds were regularly found at low spots in a canyon between two lava flows during 2001–2006, but the phenomenon was attributed to natural trapping and starvation of fledgling seabirds (mostly Least Auklets, Aethia pusilla) at a colony site with >1 million birds present. However, 302 birds of eight species, including passerines, were found dead at the site during 2007–2010, suggesting additional factors were involved. Most carcasses showed no signs of injury and concentrations of dead birds had accumulated in a few distinctive low pits in the canyon. Gas samples from these locations showed elevated CO2 concentrations in late 2010. Analysis of carcasses indicated no evidence of blunt trauma or internal bleeding. Volcanic gases accumulating at these poorly ventilated sites may have caused the observed mortality, but are temporally variable. Most auklets breeding in the Aleutian Islands do so in recent lava flows that provide breeding habitat; our study documents a cost of this unusual habitat selection.