Markerless motion capturing has the potential to provide a low-cost and accessible alternative to traditional marker-based systems for real-world biomechanical assessment. However, before these systems can be put into practice, we need to rigorously evaluate their accuracy in estimating joint kinematics for various gait patterns. This study evaluated the accuracy of a low-cost, open-source, and smartphone-based markerless motion capture system, namely OpenCap, for measuring 3D joint kinematics in healthy and pathological gait compared to a marker-based system. 21 healthy volunteers were instructed to walk with four different gait patterns:​ physiological, crouch, circumduction, and equinus gait. Three-dimensional kinematic data were simultaneously recorded using the markerless and a marker-based motion capture system. The root mean square error (RMSE) and the peak error were calculated between every joint kinematic variable obtained by both systems. We found an overall RMSE of 5.8 (SD:​ 1.8 degrees) and a peak error of 11.3 degrees (SD:​ 3.9). A repeated measures ANOVA with post hoc tests indicated significant differences in RMSE and peak errors between the four gait patterns (p ¡ 0.05). Physiological gait presented the lowest, crouch and circumduction gait the highest errors. Our findings indicate a roughly comparable accuracy to IMU-based approaches and commercial markerless multi-camera solutions. However, errors are still above clinically desirable thresholds of two to five degrees. While our findings highlight the potential of markerless systems for assessing gait kinematics, they also underpin the need to further improve the underlying deep learning algorithms to make markerless pose estimation a valuable tool in clinical settings.