Objective: Bone marrow lesions (BML) are important in established knee osteoarthritis, predicting pain and progression of disease. Whether BML are also associated with longitudinal changes in knee structure in an asymptomatic population is unknown. Methods: 148 healthy pain-free women in middle age with no history of knee injury or clinical knee osteoarthritis who had a magnetic resonance imaging (MRI) scan performed on their dominant knee at baseline, had another MRI 2 years later to assess whether having a BML present at baseline affected change in tibiofemoral cartilage defects and tibial cartilage volume. Results: BML were present in 14.9% of women at baseline. The risk of progression of total tibiofemoral cartilage defects was significantly higher when a very large BML was present (odds ratio 5.55, 95% CI 1.04 to 29.6) compared with when no BML was present, after adjusting for potential confounders. In the lateral compartment, the rate of cartilage volume loss was significantly greater when a BML was present after adjusting for confounders (regression coefficient 39.2 mm3, 95% CI 11.1 to 67.2, p = 0.007). Conclusions: In healthy women without pain at baseline, large BML were associated with both progression of cartilage defects in the whole tibiofemoral joint and more rapid lateral tibial cartilage loss. These data suggest that the relationship between BML and knee cartilage in healthy women is similar to that described in established osteoarthritis. It is possible that BML may predict an increased risk of knee osteoarthritis and facilitate the identification of novel interventions to prevent disease.