Woolly mammoths were among the most abundant cold adapted species during the Pleistocene. Their once large populations went extinct in two waves, an end-Pleistocene extinction of continental populations followed by the mid-Holocene extinction of relict populations on St. Paul Island ~5,600 years ago and Wrangel Island ~4,000 years ago. While the extinction of Wrangel Island mammoths was preceded by prolonged demographic decline, reduced population size and genetic diversity, recurrent inbreeding, and the fixation of deleterious alleles, the functional consequences of these processes are unclear. Here we show that the Wrangel Island mammoth had a large burden of deleterious mutations that are predicted to cause diverse behavioral and developmental defects. Resurrection and functional characterization of Wrangel Island mammoth genes with putative deleterious substitutions identified both loss and gain of function mutations associated with ciliopathies, oligozoospermia and reduced fertility, and neonatal diabetes. These results indicate that last mammoths likely suffered from genetic disease that reduced fitness and directly contributed to their extinction.