Subchondral bone changes seem to contribute to the progression of knee osteoarthritis (OA). The study aimed to analyze subchondral bone microstructure in specimens of late-stage knee OA in respect to articular cartilage damage, meniscus integrity and knee joint alignment. Methods and Materials: 30 proximal tibiae of 30 patients (20 female and 10 male) with late-stage OA retrieved during total knee arthroplasty (TKA) were scanned using a high-resolution MicroComputed Tomography (μCT). The scans were semi-automatically segmented into five volumes of interest (VOIs). The VOIs were than further analyzed using commercially available software. The degree of articular cartilage damage was assessed semi-quantitatively by magnetic resonance imaging (MRI) before surgery. Results: The mean bone fraction volume (BV/TV) in all weight bearing locations was significantly higher compared to the non weight-bearing reference point below the anterior cruciate ligament (p=0,000). The mean BV/TV in the medial compartment was significantly higher compared to the lateral compartment (p=0,007). The BV/TV in intact menisci, there was a significantly lower subchondral BV/TV compared to subluxated or luxated menisci in the medial (p=0,020) and lateral compartment (p=0,005). Varus alignment had a significantly higher subchondral BV/TV in the medial compartment, whereas valgus alignment had a significantly higher subchondral BV/TV in the lateral compartment (p=0,011). Conclusion: The results show significant differences of subchondral bone microstructural parameters in respect to cartilage damage, meniscus’ structural integrity and knee joint alignment. Therefore, subchondral bone changes seem to be a secondary process in the late-stage OA of knee caused by mechanical changes.