Deciding whether or not to extract third molars remains a controversial situation in dental practice. Image exams support this decision by enabling a close view of the third molar, its adjacent bone and its relationship with the second molar. This study aimed to assess and compare second molar bone loss adjacent to impacted mandibular third molar in panoramic radiographs (PAN) and cone beam computed tomography (CBCT) scans. A sample of 70 patients was selected (n=124 teeth). Each patient had a set of a panoramic radiograph and CBCT scans consecutively taken for dental treatment purposes. In PAN and CBCT, mandibular third molars were classified based on their position and bone loss of the adjacent second molar. Agreement between PAN and CBCT scans was assessed and quantified. Outcomes of bone loss assessment were different between PAN and CBCT scans (p<0.05). Bone loss was found in 62.9% of the PAN, while in CBCT scans it was found in 80%. In particular, nearly 29% (n=27) of the teeth that were classified without bone loss in PAN were classified with bone loss in CBCT scans. Mesioangular and horizontal third molars had a statistically significant association with bone loss of the adjacent second molars (p<0.05). In general, PAN underestimated the severity of bone loss compared to CBCT scans (p<0.05). Diagnosing second molar bone loss due to impaction of adjacent third molar in PAN may be challenging because of false negatives. Impacted third molars justify preoperative CBCT scans if second molar bone loss needs to be precisely assessed for a more detailed and reliable treatment plan.