Background Coronal malalignment of the lower extremity is closely related to the onset and progression of osteoarthritis. Restoring satisfactory alignment after tibial osteotomy improves the long-term success of this conservative surgery. The purpose of our study was to determine (1) if there is a difference between two-dimensional (2D) and 3D measurements of the hip-knee-ankle (HKA) angle between the mechanical axes of the femur and the tibia, (2) which parameter most affects 2D-3D HKA measurement, and (3) the percentage of patients who are at risk of error in HKA measurement. Methods We reviewed imaging studies of the consecutive patients referred to us for hip or knee pain between June and October 2013. Patients with previous pelvis or lower extremity surgery were excluded. Results In 51 % (95/186) of lower extremities examined, the 3D method showed more valgus than the 2D method, and in 49 % (91/186), the 3D method showed more varus. In 12 % of extremities (23/186), the knee varus or valgus alignment was completely opposite in 3D images compared to 2D images. Having more than 7A degrees of flexum/recurvatum alignment increased error in 2D HKA measurement by 5.7A degrees. This was calculated to be 0.15A degrees per 1A degrees increase in femoral torsion and 0.05A degrees per 1A degrees increase in tibial torsion. Approximately 20 % of patients might be at risk of error in HKA angle measurement in 2D imaging studies. Conclusions Orthopaedic surgeons should assess lower extremity alignment in standing position, with enough exposure of the extremity to find severe alignment or rotational deformities, and consider advanced 3D images of those patients who have them. Otherwise, HKA angle can be measured with good accuracy with 2D techniques.