Introduction Three-dimensional gait analysis (3DGA) in obese populations is a difficult task due to a great amount of subcutaneous fat. This makes it more challenging to identify anatomical landmarks, thus leading to inconsistent marker placement. Therefore, the purpose of this study was to investigate the test-retest reliability for kinematic measurements of obese children and adolescents. Methods Nine males and two females with an age-based BMI above the 97th percentile (age: 14.6 ± 2.6 years, BMI: 33.4 ± 4.4 kg/m 2 ) were administered to two 3DGA sessions. To quantify reliability of discrete parameters the intraclass correlation coefficient (ICC 2,k ), standard error of measurement (SEM) and minimal detectable change (MDC) were calculated. To quantify waveform similarity, the coefficient of multiple correlation (CMC) and the linear fit method (LFM) were used. Results From 28 kinematic parameters, 23 showed acceptable ICCs (≥0.70) and the remaining parameters demonstrated moderate values. These were peak hip extension during stance (0.58), mean pelvis rotation (0.60), mean anterior pelvic tilt (0.64), peak knee flexion during swing (0.67) and peak hip abduction during swing (0.69). The SEM was below 5° for all parameters. The MDC for the sagittal, frontal, and transversal plane were on average 7.5° ± 2.2, 4.6° ± 1.3 and 6.0° ± 0.9 respectively. Both the LFM and CMC showed, in general, moderate to good reliability except for pelvis tilt and hip rotation. Conclusion Data demonstrated acceptable error margins especially for the sagittal and frontal plane. Low reliability for the pelvis tilt indicates that great effort is necessary to position the pelvic markers consistently during repeated sessions.