Aleutian Tern Onychoprion aleuticus numbers have been in steep decline at known Alaskan breeding colonies in recent decades (IUCN recently uplisted to ‘Vulnerable’). Available data suggest that most of the species may currently breed in Russia. Efforts to document global abundance and trends have been hampered by remoteness of colonies, lack of a formal monitoring programme, and the absence of reproducible population estimates with quantifiable errors, especially for large colonies. We surveyed four historically large colonies in Russia (2018) and Alaska (2019), which together may comprise 30–50% of the global breeding population. At each colony we obtained high resolution aerial photographs using a small Unmanned Aircraft System (sUAS). The large size of the colonies and the minimum altitude required to identify terns made it impractical to collect imagery of the entire colony. Instead, we employed a sampling approach, with sample locations selected based on spatially balanced acceptance sampling. Statistically sampled, low altitude sUAS images provided a fast, reproducible, and rigorous count of abundance for geographically large colonies, with low disturbance, and were generally consistent with concurrent ground-based observations. Concurrence among observers in photo counts indicated high precision in counts of attending birds and unattended nests, although species attribution in mixed tern colonies remains a source of significant uncertainty. Our results indicate that the four colonies surveyed here together supported <2,500 pairs of Aleutian Terns in the survey years. None of the colonies approached their peak size reported previously, likely due to recent predation, long-term decline, cold early season weather, or other factors. If these reduced colony sizes are representative of the current conditions, the implications for the global population would be dire.