Infections play an important role in childhood. For Germany, few data are available on the epidemiology of infectious diseases such as otitis media and pneumonia in children. We therefore described the prevalence, first episode proportions and recurrence of these childhood infection diseases in selected regions of Germany in children up to 6 years of age. The analysis was based on data from the LISA Study, a prospective population-based birth cohort study including 3,097 full-term infants. Information was collected by parent questionnaire. The first episode proportions for the first 6 years of life were high for otitis media (66.7%; 95%CI 0.65-0.69) and pneumonia (13.5%; 95%CI 0.12-0.15). The annual first episode proportions for otitis media ranged from 7.3% to 25.6% and for pneumonia from 1.4% to 3.4%; both peaked during the second year. The average number of otitis media episodes was 2.2 (SD 2.0) episodes per child within the first 2 years. During the first 2 years of life, hospitalisations due to otitis and pneumonia occurred in up to 7.8 per thousand and 3.0 per thousand of the children, respectively. On average, 50.6% of the children with otitis media were treated with antibiotics during the first year of life. In conclusion, this analysis shows that infectious diseases, especially otitis media, are very frequent childhood diseases in Germany. Thus, parents and physicians should not per se worry about a high frequency of otitis media during early childhood.