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Background: Infrared thermography is an aid tool that can be used to evaluate several pathologies given its efficiency in analyzing the distribution of skin surface temperature. Objectives: To propose two forms of infrared image analysis of the masticatory and upper trapezius muscles, and to determine the intra and inter-rater reliability of both forms of analysis. Method: Infrared images of masticatory and upper trapezius muscles of 64 female volunteers with and without temporomandibular disorder (TMD) were collected. Two raters performed the infrared image analysis, which occurred in two ways: temperature measurement of the muscle length and in central portion of the muscle. The Intraclass Correlation Coefficient (ICC) was used to determine the intra and inter-rater reliability. Results: The ICC showed excellent intra and inter-rater values for both measurements: temperature measurement of the muscle length (TMD group, intra-rater, ICC ranged from 0.996 to 0.999, inter-rater, ICC ranged from 0.992 to 0.999; control group,intra-rater, ICC ranged from 0.993 to 0.998, inter-rater, ICC ranged from 0.990 to 0.998), and temperature measurement of the central portion of the muscle (TMD group, intra-rater, ICC ranged from 0.981 to 0.998, inter-rater, ICC ranged from 0.971 to 0.998; control group, intra-rater, ICC ranged from 0.887 to 0.996, inter-rater, ICC ranged from 0.852 to 0.996). Conclusion: The results indicated that temperature measurements of the masticatory and upper trapezius muscles carried out by the analysis of the muscle length and central portion yielded excellent intra and inter-rater reliability. [ABSTRACT FROM AUTHOR]