In palaeopathological research, otitis media (OM) is a rarely reported disease, although it is one of the most common diseases of childhood, with potentially severe consequences resulting in physical and social impairment, or even death. The episodes of OM are often preceded by upper respiratory tract infections, though the aetiology of OM is multifactorial, with significant role of environmental factors. In archaeological skeletons, middle ear inflammation is identified as erosive lesions and new bone formation of auditory ossicles. The aim of this study was to examine the skeletal signs of OM in children from a mediaeval early urban site (Cedynia) and a post‐mediaeval rural site (Słaboszewo) located on the territory of Poland. Among the entire sample (N = 435), ear bones were present in 99 skeletons. The total of 168 ossicles were examined. The general frequency of individuals with eroded ossicles was 47.5% (53.4% in Cedynia and 39.0% in Słaboszewo). In the total sample, 33.9% of ear bones showed pathological changes, with the incudes being most frequently affected. The frequency of altered ossicles was significantly higher in the early urban site than in the rural settlement (42.2% vs 25.9%, respectively; Fisher exact test, p = 0.0339). The children aged 0–3 years old tend to have a higher frequency of altered ear bones than the children aged 4–11 years old. The majority of the mastoid processes of the subadults with ear bone erosion show abnormal pneumatisation pattern. The results indicate that the environmental and socio‐cultural conditions in the stronghold likely made their inhabitants more prone to upper respiratory tract infections than the inhabitants of the village. A variety of factors may be responsible for this pattern, such as exposure to dust, environmental pollution, indoor pollution, wood smoke, occupation, population density, sanitation and quality of housing. Copyright © 2016 John Wiley & Sons, Ltd.