Introduction: The aim of this cross-sectional epidemiological study was to record caries and enamel hypomineralisation (EH), including molar-incisor hypomineralisation (MIH), and assess associations between both entities in 8- to 10-year-olds from Bavaria, Germany. Methods: A total of 5,418 children (mean age 9.8 years; 2,726 females, 2,692 males) were examined using the dmft/DMFT index with additional inclusion of initial or non-cavitated carious lesions (it/IT). EHs were recorded in the primary (eh) and permanent dentition (EH), and individuals with different EH phenotypes were determined as follows: at least one EH, at least one hypomineralised second primary molar (HSPM), at least one hypomineralised first permanent molar (MIH), and at least one hypomineralised first permanent molar and incisor (M+IH). Multiple logistic regression models were constructed to assess association between caries and EH. Results: The percentage of children without caries in the permanent dentition (DMF = 0) was 88.9%. When data regarding initial carious lesions were included (IDMF = 0), the prevalence decreased to 75.7%. The caries experience was idmf/t = 1.6 and the IDMF/T = 0.6. The mean number of carious teeth in subjects with no eh/EH was higher than that in subjects with HSPM, MIH, or M+IH. The presence of HSPM, MIH, and M+IH was associated with a significantly lower probability of caries in the permanent dentition; the corresponding adjusted odds ratios were 0.55 (95% CI: 0.41−0.75), 0.67 (95% CI: 0.56−0.81), and 0.54 (95% CI: 0.41−0.72), respectively. Conclusions: Caries and EH are prevalent conditions in 8- to 10-year-old Bavarian schoolchildren; both dental diseases were negatively associated with each other.