Objectives The aim of this study is to investigate the effect of internal derangements and degenerative bone changes on the minimum thickness of the roof of the glenoid fossa (RGF). Methods MRI and cone beam CT records of temporomandibular joints (TMJ) of 68 patients were evaluated retrospectively in this study. The joints were divided into three groups according to TMJ disc status which had been diagnosed in MRI: normal disc status, anterior disc displacement with reduction, and anterior disc displacement without reduction. Cone beam CT was used to evaluate the degenerative bone changes of TMJ and to measure the minimum thickness of RGF. The joints were categorized as "with osteoarthritis (OA)" or "without OA". The findings of OA were determined as erosion, osteophyte, flattening, sclerosis, and pseudocyst. Results No significant relationship was found between gender and the thickness of RGF (p > 0.05). RGF was found significantly higher in "with OA" group compared to "without OA" group (p < 0.001). No significant difference was found between disc displacement groups for minimum thickness of RGF (p > 0.005). No significant difference was found between condyles without erosion and condyles with erosion for the minimum thickness of RGF (p = 0.272). In the present study, osteophyte, sclerosis, flattening, and pseudocyst were found to be associated with the minimum thickness of RGF. Conclusions Osteophyte, flattening, pseudocyst, and sclerosis have an influence on RGF thickness. The minimum thickness of RGF is not significantly correlated with internal derangements. Erosion is not significantly correlated with RGF thickness. RGF thickness may be unaffected by the early stages of OA.