OBJECTIVE The aim of the present cross-sectional study was to assess and compare the prevalence of MIH among 6-12-year-old school children living either in a rural area of Central Hesse (Germany) or in the city of Frankfurt on the Main (Germany). A possible association between hypomineralised second primary molars (HSPM) and MIH was investigated. Furthermore, the MIH prevalence data of the rural area were compared with those of a previous study conducted in this area in the school year 2002/2003. METHODS In the school year 2014/2015, 2103 children (6-12 years of age) were examined during the annual school-based dental examinations prescribed by law at nine schools in the rural area of Central Hesse (LDK) and five schools in the city of Frankfurt on the Main (Ffm). Eight previously calibrated dentists working for the public healthcare authorities assessed the prevalence of HSPM/MIH (EAPD criteria/severity scale by Wetzel and Reckel) and the caries experience (dmft/DMFT). RESULTS The prevalence of HSPM/MIH amounted 3.2%/9.4% in LDK and 2.9%/17.4% in Ffm. In the majority of cases, children with MIH had demarcated opacities. In LDK, hypomineralised first permanent molars were most commonly affected by severity degree 2, whereas in Ffm, severity degree 1 was predominant. Children suffering from HSPM had an odds ratio of 11.32 (95% CI: 6.73-19.03) for having MIH as well. Compared with the results of 2002/2003 in LDK (prevalence of MIH 5.9%), the MIH prevalence increased by 3.5% in the rural area. All in all, the caries experience among children under investigation was low (DMFT 0.14-0.15). CONCLUSIONS MIH may be diagnosed in school children living in different areas of Germany with regional variations (rural-urban comparison). The presence of HSPM is of predictive value for MIH. The increasing number of hypomineralised first permanent molars over 12 years of time in the rural area indicates a need for further investigation on the aetiology of MIH.