There are seven emperor penguin (Aptenodytes forsteri) colonies distributed throughout the traditional boundaries of the Ross Sea from Cape Roget to Cape Colbeck. This coastline is c. 10% of the entire coast of Antarctica. From 2000 to 2012, there has been a nearly continuous record of population size of most, and sometimes all, of these colonies. Data were obtained by analysing aerial photographs. We found large annual variations in populations of individual colonies, and conclude that a trend from a single emperor penguin colony may not be a good environmental sentinel. There are at least four possibilities for census count fluctuations: i) this species is not bound to a nesting site like other penguins, and birds move within the colony and possibly to other colonies, ii) harsh environmental conditions cause a die-off of chicks in the colony or of adults elsewhere, iii) the adults skip a year of breeding if pre-breeding foraging is inadequate and iv) if sea ice conditions are unsatisfactory at autumn arrival of the adults, they skip breeding or go elsewhere. Such variability indicates that birds at all Ross Sea colonies should be counted annually if there is to be any possibility of understanding the causes of population changes.