White-chinned petrels Procellaria aequinoctialis and grey petrels Procellaria cinerea are among the most frequently killed seabird species by accidental bycatch, and both species have received strong conservation concern. Data on population size are required to evaluate the impact of bycatch and to establish management plans. We estimated the population size of both species at Kerguelen, Southern Indian Ocean, from 2004 to 2006 by explicitly taking into account detection probability of burrows using distance sampling and burrow occupancy. A total of 31 line-transects were distributed across the eastern part of Kerguelen, representing a total length of 566 km. Detectability was low (from 0.19 to 0.54 for white-chinned petrels, 0.58 for grey petrels). Burrow densities varied from 1.37±0.67 to 25.77±5.23 burrows ha−1 for white-chinned petrels and was 2.78±0.79 burrows ha−1 for grey petrels. For white-chinned petrels, these densities were extrapolated to the entire surface area of vegetation and there were 234 000 (186 000–297 000) active burrows on Kerguelen. For grey petrels, the number of active burrows for the eastern part of Kerguelen was 3400 (1900–5600). Based on these estimates, the potential biological removal method suggests that the additional mortality on birds caused by the fisheries operating around Kerguelen can be considered a serious threat for the species at least at the regional scale of the Southern Indian Ocean, especially for grey petrels.