This epidemiological study aimed to compare the caries and molar incisor hypomineralisation (MIH) experience in asthmatic and non-asthmatic adolescents assessed at 10 and 15 years of age. 730 adolescents from ongoing birth cohort studies (GINIplus/LISA) from Munich, Germany, were examined for carious lesions at the age of 10 and 15 years to determine caries experience under inclusion of non-cavitated carious lesions D<sub>1–2</sub>T and the tooth-related decay-missing-filled index. Furthermore, MIH was scored on all permanent teeth according to the criteria of the European Academy of Paediatric Dentistry. The association between caries and MIH prevalence at the 10-year and 15-year follow-up as well as caries incidence with ever having an asthma diagnosis was analysed using hurdle regression models adjusted for potential confounders. Of the 730 adolescents, 52 and 78 were identified as asthmatics at the 10- and 15-year follow-up, respectively. There were no significant differences in caries prevalence or experience between asthma-free participants and any of the asthma groups (taking metered-dose inhaler (MDI) medication vs. taking no MDI medication). However, a significant positive association was found for asthmatic adolescents who did not take MDI medication with higher MIH/T values (OR = 2.56, 95% CI = 1.03–6.37, p = 0.043) compared to non-asthmatics. In conclusion, asthma did not influence the caries status of adolescents in the present study. Interestingly, a significant association was found between adolescents with asthma who did not take MDI medication and the number of MIH-affected teeth. The association between asthma, medication, and MIH needs further confirmation.