Dogs with cranial cruciate ligament rupture (CCLR) are at high risk for subsequent contralateral rupture. The disease process is likely multifactorial, and breed predispositions may be present. To date, there are no established preventative therapies to reduce the risk for CCLR in high-risk dogs. In laboratory models of CCLR, doxycycline has been shown to reduce osteoarthritis severity and inhibit degenerative collagenase activity. This prospective, randomized, controlled clinical trial investigated the effect of doxycycline on rate of contralateral CCLR (Co-CCLR) in dogs. Sixty-nine dogs were enrolled with unilateral CCLR and a stable contralateral stifle joint. Treated dogs (n = 32) received doxycycline (7.5 mg/kg PO twice a day) for 6 weeks following TPLO of the unstable stifle joint. Dogs were monitored for 4 to 5 years to determine if Co-CCLR occurred. There was no treatment effect of doxycycline on the rate of Co-CCLR; Co-CCLR occurred in 53.1% and 48.6% at medians of 20 and 11 months in treated and control dogs, respectively. Increasing age decreased risk for rupture by 14.2% for each year. With every increasing kilogram of body weight and degree of tibial plateau angle, risk for rupture increased by 5.4% and 9.7%, respectively. Labrador retrievers were not significantly predisposed to CCLR.