Background Dentinogenesis imperfecta (DGI) is a heritable disorder of dentin. Genetic analyses have found two subgroups in this disorder: DGI type I, a syndromic form associated with osteogenesis imperfecta (OI), and DGI type II, a non-syndromic form. The differential diagnosis between types I and II is often challenging. Thus, the present cross-sectional study had two aims: to (i) investigate the prevalence and incidence of DGI type II among Swedish children and adolescents and (ii) search out undiagnosed cases of DGI type I by documenting the prevalence of clinical symptoms of OI in these individuals. We invited all public and private specialist pediatric dental clinics (n = 47) in 21 counties of Sweden to participate in the study. We then continuously followed up all reported cases during 2014−2017 in order to identify all children and adolescents presenting with DGI type II. Using a structured questionnaire and an examination protocol, pediatric dentists interviewed and examined patients regarding medical aspects such as bruising, prolonged bleeding, spraining, fractures, hearing impairment, and family history of osteoporosis and OI. Joint hypermobility and sclerae were assessed. The clinical oral examination, which included a radiographic examination when indicated, emphasized dental variables associated with OI. Results The prevalence of DGI type II was estimated to be 0.0022% (95% CI, 0.0016–0.0029%) or 1 in 45,455 individuals. Dental agenesis occurred in 9% of our group. Other findings included tooth retention (17%), pulpal obliteration (100%), and generalized joint hypermobility (30%). Clinical and radiographic findings raised a suspicion of undiagnosed OI in one individual, a 2-year-old boy; he was later diagnosed with OI type IV. Conclusions These results show a significantly lower prevalence of DGI type II than previously reported and point to the importance of excluding OI in children with DGI. Electronic supplementary material The online version of this article (10.1186/s13023-018-0887-2) contains supplementary material, which is available to authorized users.