An irregular contour of the medial femoral condyle (MFC) on magnetic resonance imaging (MRI) appears to indicate the severity of medial-type knee osteoarthritis (OA). The purpose of this study was to establish a system to enable objective assessments of OA knee severity using newly developed software that semi-automatically measures irregularity of the MFC. (1) We evaluated 48 patients aged 50-83 years with 55 knees of medial-type OA. The following scores were recorded: Lysholm score, visual analogue scale (VAS) and the Japanese Knee Osteoarthritis Measure (JKOM). MFC irregularity was automatically calculated by newly programmed computer software. Four parameters for condyle irregularity were calculated: (a) the average thickness of the contour (ATC), (b) the ratio of the upper surface length to the lower surface length of the contour (RUL), (c) average squared thickness of the contour (ASTC) and (d) standard deviation of the contour thickness (SDC). (2) Nine knees that underwent total knee arthroplasty were further analysed histopathologically and compared with irregularity score. Statistically, the RUL and SDC were significantly correlated with the Lysholm score, VAS and JKOM, with good reliability. Histological examinations showed that an irregular contour reflected the density of cystic lesions formed in subchondral bone. An irregularity of MFC on MRI is correlated with OA disease severity clinically and histopathologically. The new computer software is useful to objectively assess OA disease severity.