The 2022 highly pathogenic avian influenza (HPAI) outbreak that occurred in many European countries affected several seabird species. Among them, northern gannets (Morus bassanus) were particularly impacted. We conducted aerial surveys in waters around the two largest gannet colonies in southwest Ireland (Little Skellig and Bull Rock, together representing 87% of the national population) in September 2022. During surveys dead and alive northern gannets were counted on survey effort. A total of 184 dead gannets were recorded on survey effort, representing 3.74% of the total number of gannets recorded. We estimated the abundance of dead gannets in the surveyed area at 1526 (95% confidence intervals (CIs) 1450–1605) individuals. The percentage of dead gannets observed was used to estimate a minimum local population mortality of 3126 (95% CIs 2993–3260) individuals across both colonies. Aerial surveys provided key information on gannet mortality from HPAI at sea. The study provides the first estimate of gannet mortality in the two largest gannetries in Ireland.