Background: The greater trochanter marker is commonly used in 3-dimensional (3D) models; however, its influence on hip and knee kinematics during gait is unclear. Understanding the influence of the greater trochanter marker is important when quantifying frontal and transverse plane hip and knee kinematics, parameters which are particularly relevant to investigate in individuals with conditions such as patellofemoral pain, knee osteoarthritis, anterior cruciate ligament (ACL) injury, and hip pain. The aim of this study was to evaluate the effect of including the greater trochanter in the construction of the thigh segment on hip and knee kinematics during gait. Methods: 3D kinematics were collected in 19 healthy subjects during walking using a surface marker system. Hip and knee angles were compared across two thigh segment definitions (with and without greater trochanter) at two time points during stance: peak knee flexion (PKF) and minimum knee flexion (MinKF). Results: Hip and knee angles differed in magnitude and direction in the transverse plane at both time points. In the thigh model with the greater trochanter the hip was more externally rotated than in the thigh model without the greater trochanter (PKF: −9.34° ± 5.21° vs. 1.40° ± 5.22°, MinKF: −5.68° ± 4.24° vs. 5.01° ± 4.86°; p < 0.001). In the thigh model with the greater trochanter, the knee angle was more internally rotated compared to the knee angle calculated using the thigh definition without the greater trochanter (PKF: 14.67° ± 6.78° vs. 4.33° ± 4.18°, MinKF: 10.54° ± 6.71° vs. −0.01° ± 2.69°; p < 0.001). Small but significant differences were detected in the sagittal and frontal plane angles at both time points (p < 0.001). Conclusion: Hip and knee kinematics differed across different segment definitions including or excluding the greater trochanter marker, especially in the transverse plane. Therefore when considering whether to include the greater trochanter in the thigh segment model when using a surface markers to calculate 3D kinematics for movement assessment, it is important to have a clear understanding of the effect of different marker sets and segment models in use.