Introduction: Magnetic resonance imaging (MRI) is considered the examination of choice for the diagnosis of abnormalities in the TMJ. Considering the difficulty in defining and standardizing the diagnostic criteria, and the need for more accurate and reliable diagnosis of conditions in the TMJ, the aim of the present study was to compare three different MRI parameters: T1-weighted, T2-weighted and proton density–weighted in the diagnosis of changes in the temporomandibular joint. Materials and Methods: Fifty magnetic resonance imaging examinations of the temporomandibular joint (100 temporomandibular joints) were conducted according to a protocol that evaluates disc position, disc function and bone abnormalities. The images were obtained bilaterally in parasagittal sections in closed and open mouth positions in the three studied parameters Three trained oral radiologists assessed all the images. Reliability of the intra- and inter-examiner response was analyzed using the concordance test (Fleiss’ kappa; α = 0.05). Results: The reliability of the response patterns between observers for different protocols varied from very good to good. Observers were less constant in their response patterns when assessing proton density–weighted images. There was very good agreement for disc morphology, cortical bone and bone structures/functions; however, there was wide variation for medullary bone marrow signs. Conclusion: T2-weighted imaging was found to be the best examination to assess the medullary bone. For evaluating of disc morphology, cortical bone and bone structures/functions, any protocol is indicated once the protocol does not interfere with the analysis.