© 2016 Objective To illustrate and discuss sources of gait deviations (experimental, genuine and intentional) during a gait analysis and how these deviations inform clinical decision making. Methods A case study of a 24-year old male diagnosed with Alkaptonuria undergoing a routine gait analysis. A 3D motion capture with the Helen-Hayes marker set was used to quantify lower-limb joint kinematics during barefoot walking along a 10 m walkway at a self-selected pace. Additional 2D video data were recorded in the sagittal and frontal plane. The patient reported no aches or pains in any joint and described his lifestyle as active. Results Temporal-spatial parameters were within normal ranges for his age and sex. Three sources of gait deviations were identified; the posteriorly rotated pelvis was due to an experimental error and marker misplacement, the increased rotation of the pelvis in the horizontal plane was genuine and observed in both 3D gait curves and in 2D video analysis, finally the inconsistency in knee flexion/extension combined with a seemingly innocuous interest in the consequences of abnormal gait suggested an intentional gait deviation. Conclusions Gait analysis is an important analytical tool in the management of a variety of conditions that negatively impact on movement. Experienced gait analysts have the ability to recognise genuine gait adaptations that forms part of the decision-making process for that patient. However, their role also necessitates the ability to identify and correct for experimental errors and critically evaluate when a deviation may not be genuine.