Objectives. Meniscal extrusion is often present in knees with OA, and has been associated with cartilage changes. It is unknown whether meniscal extrusion is related to subchondral bone. The aim of the study was to examine the relationship between meniscal extrusion and knee cartilage and subchondral bone, and also changes in these structures over 2 years in a cohort with mild to moderate knee OA. Methods. One hundred and seventeen subjects with knee OA entered the study and underwent MRI on their symptomatic knee at baseline and ∼2 years later. Meniscal extrusion was assessed at baseline; tibial cartilage volume and plateau bone area, subchondral bone marrow lesions (BMLs) and bone cysts were measured at baseline and follow-up. Results. At baseline, meniscal extrusion was associated with reduced tibial cartilage volume, increased tibial plateau area, increased prevalence of BMLs and bone cysts in both medial and lateral tibiofemoral compartments (all P ⩽ 0.001). Baseline medial meniscal extrusion was associated with increased expansion of tibial plateau bone (P = 0.04), increases in BMLs (P = 0.02) and bone cysts (P = 0.003) in the medial tibiofemoral compartment over 2 years. Conclusions. Meniscal extrusion predicts increases in subchondral bone lesions and tibial plateau bone expansion in patients with knee OA. These data suggest that subchondral bone changes are an early consequence of meniscal extrusion. This may reflect the impaired ability of an extruded meniscus to optimally distribute mechanical loading across the tibial plateau.