Otitis media occurs frequently among modern Greenlanders. However, knowledge of the epidemiology of this disease before the twentieth century is scanty. Information on diseases in the past may give us a better understanding of the health of historical populations. This study presents a new unbiased method for estimating the incidence of infectious middle ear disease (IMED) in childhood. The method is based on the relationship between IMED in childhood and morphological evidence present in the human temporal bones - i.e. small or asymmetrical pneumatized cell areas.In a standardized X-ray projection, we examined 434 pneumatized cell areas in temporal bones from 34 living adult modern Greenlanders, 56 historical adult Greenland Eskimo crania from the period after the European colonization of Greenland in 1721 AD, and 127 prehistoric adult Greenland Eskimo crania from the period before the colonization. The resulting X-rays of the crania were of high quality and the relationship between IMED in childhood and small or asymmetrical pneumatized cell areas was confirmed in the modern Greenlanders. On this basis a polychotomous logistic regression model was applied to the pneumatized cell areas of the three groups of material. The model allowed for the interdependence of the ears and specified probabilities of having IMED in the right ear, left ear, both ears or of being healthy in both ears.The frequency of IMED as indicated by the model was 8/34 (23.5%) in modern Greenlanders, 10/56 (17.9%) in historical Eskimo crania and 6/127 (4.7%) in prehistoric Eskimo crania (p < 0.002). The mean area also differed significantly, as it was smallest in modern Greenlanders. The results thus indicated a change in the frequency of IMED and a decrease in area from historical to present-day Greenland in subjects who survived to adulthood. The change seemed closely related to the European colonization of Greenland. As IMED is closely related to upper respiratory tract infections and to poverty, the method seems well suited for evaluating general health in past societies.