Background: Although magnetic resonance imaging is accurate, it is expensive to measure the movement of temporomandibular joint. The three-dimensional (3D) motion analysis system is an inexpensive measurement tool. Objects: This study examined the reliability of quantifying the mouth opening and lateral mandibular shift and differences between individuals with and without temporomandibular disorder (TMD) using the hygienic method of surface markers on the skin with 3D ultrasound-based motion analysis. Methods: This study included 24 subjects (12 with and 12 without TMD). Temporomandibular joint motion during mouth opening was recorded using two surface markers with 3D ultrasound-based motion analysis. An intraclass correlation coefficient [ICC (3,k)] was used to confirm the intrarater reliability of quantifying kinematic temporomandibular joint motion, and an independent t-test was used to evaluate differences in maximal mouth opening and lateral mandibular shift between the two groups. Results: Assessment of mouth opening and lateral mandibular shift showed excellent test–retest reliability with low standard error of measurement. The lateral mandibular shift and opening-lateral mandibular shift ratio were significantly increased in the TMD group during maximum mouth opening (p<.05). However, no significant difference in maximal mouth opening was observed between the groups with and without TMD (p>.05). Conclusion: This hygienic and simple surface marker method can be used to quantify the mouth opening and lateral mandibular shift at the end-range of mouth opening. The TMD group showed an increased lateral mandibular shift movement at the end-range of mouth opening. The lateral mandibular shift movement can be regarded as a symptom in the diagnosis and treatment of TMD.