Purpose: The course of post-traumatic osteoarthritis (OA) is an invaluable paradigm for discovery of markers of the very earliest stages of the OA disease process. Subchondral bone trabecular integrity (BTI) predicts structural progression of radiographic knee OA based on radiographic and MRI outcomes. The goal of this study was to determine if the BTI in a knee injury cohort, measured within 5 weeks after an anterior cruciate ligament (ACL) tear, is an early indicator of risk for development of OA over the subsequent 5 years. We hypothesized that thinning and loss of the subchondral vertical bone trabeculae, detected by BTI, would predict joint space width and joint space area loss. Methods: Bone trabecular integrity (BTI) of the medial tibial plateau was determined from analysis of knee radiographs from the completed randomized controlled KANON clinical trial (http://www.controlled-trials.com; ISRCTN 84752559), designed to compare rehabilitation plus early ACL reconstruction (ACLR, n = 61) versus rehabilitation plus optional delayed ACLR (n = 60) with follow-up out to 5 years. The KANON study enrolled 121 young active adults (aged 18–35 yrs) with acute ACL rupture within the prior 5 weeks to a previously uninjured knee. There was no loss to follow-up at 2 years and only 1 individual lost to follow-up at 5 years; none of the index knees had radiographic OA at baseline. Weight bearing knee radiographs, obtained at baseline (at time of enrollment), 2 years and 5 years using a modified Lyon-Schuss protocol, were analyzed using KneeAnalyzer software (Optasia Medical Ltd, Manchester, UK) to obtain fractal dimensions for computing BTI, minimum medial joint space width (mJSW), and medial joint space area (JSA). Multivariable regression models, adjusted for age, gender and body mass index, were used to evaluate the ability of baseline (BL) BTI parameters of index knees to predict the change in mJSW and JSA between BL and 2 y and 5 y after injury. Results: Based on BTI profiles injured knees on average showed thinning of vertical trabeculae over 2 years with further thinning between 2 and 5 years. Horizontal trabeculae showed thickening over 2 years with little further change to 5 years. Baseline BTI parameters were statistically significantly associated with change in mJSW over 2 (R2 0.19, p = 0.036) and 5 (R2 0.16, p = 0.04) years, and change in JSA over 5 (R2 0.22, p = 0.004), but not 2 (R2 0.13, p = 0.16) years. Conclusions: The qualitative changes in BTI parameters over time after injury, reflecting vertical and horizontal trabecular structure, were similar to changes earlier reported over similar time intervals in knee OA progressors. The remarkable finding that baseline BTI predicted subsequent changes in mJSW and JSA suggests that acute injury leads to dramatic acute alterations in bone structure, and/or, that pre-injury BTI identifies and perhaps contributes to, risk of knee injury. Longitudinal surveillance, initiated prior to injury, is needed to determine if BTI might identify individuals at high-risk for post-injury OA and who could be targeted with interventions to prevent subsequent development of OA.