Arctic Terns show large variations in colony attendance between breeding seasons, making comparable counts of colony size complex and population status estimates difficult. Here, three areas in two regions of Greenland were surveyed in consecutive breeding seasons between 2002 and 2009. Between-year variation in population size in the small and mid-sized Arctic Tern colonies in West Greenland was considerable (mean CV of individual colonies 117.5%, CV of total 49.6%). In the largest colony in Greenland, Kitsissunnguit, overall colony size showed minor variations (CV 14.6%), but variation in numbers was pronounced at the sub-colony level (mean CV 47.4%). When combining the surveyed colonies in West Greenland, the total population size varied little (CV 6.7%) and less than expected if colonies fluctuated independently (P = 0.023), indicating that local movements between the colonies took place and annual variation was linked to local rather than to large-scale phenomena. In Northeast Greenland, complete breeding failure, likely caused by Arctic Fox, was recorded in two out of four seasons. Future Greenland Arctic Tern colony monitoring should either 1) survey multiple colonies within the same season covering adjoining colonies over a larger area, or 2) survey one large, representative colony in multiple years in order to track potential changes in population size.