Bone marrow lesions (BMLs) on magnetic resonance (MR) images in knee osteoarthritis patients are considered to predict the severity and progression of the disease. We evaluated the histological findings of BMLs on MR images of the subchondral area of the medial femoral condyle in varus osteoarthritic knees. In 24 patients with varus knee osteoarthritis who underwent total knee arthroplasty (TKA), sagittal T1- and T2-weighted MR images of the affected knee were acquired before TKA. During TKA, resected bone pieces from the distal medial femoral condyle were obtained. Sagittal specimens obtained from the center of the bone pieces were histologically examined. Twenty patients had BMLs. Histological findings of BMLs in the subchondral area showed various features, such as fibrovascular tissue, cyst formation, active bone remodeling with bone formation and bone resorption, and hyaline cartilage. BMLs were not found in four patients;histological findings of these patients showed normal bone marrow tissue with normal-thickness trabeculae. Subchondral bony end plate in knees with BMLs was usually thin or destroyed, while that without BMLs was thick or normal. The condition of the subchondral bony end plate would explain the differences in the severity and progression between patients with or without BMLs.