AIM: The aim of this study was to clarify the association between impacted or erupted third molars and periodontal pathology, assessed by probing depth (PD) and clinical attachment levels (CAL), in adjacent second molars. MATERIALS AND METHODS: Data from the population-based Study of Health in Pomerania (SHIP) was used. This is the first project with whole-body magnetic resonance imaging (WB-MRI) application in a general population setting with dental issues. Calibrated and licensed dentists measured PD and CAL with a periodontal probe. RESULTS: In the mandible, individuals with erupted third molars had a 1.45-fold higher odds ratio (CI:1.03; 2.05; p = 0.031) and individuals with impacted third molars had a 2.37-fold higher odds ratio (CI:1.45; 3.85; p < 0.001) to have higher PD values in the adjacent distal site of second molar than individuals with missing third molars in the total population. These significant associations were even more pronounced in the population free of periodontitis disease. In participants with periodontitis in the maxilla, there was an association of erupted third molars with an increased PD of adjacent molars. CONCLUSION: In particular, in the mandible, those findings could guide dental practitioners more in the direction to remove the third molars after having evaluated the periodontium of the adjacent teeth.