Objective: The primary objective of this study was to compare the long-term (1-year follow-up) effects of the McKenzie method and motor control exercises on trunk muscle thickness in people with chronic low back pain (LBP) and a directional preference. Design: Randomized controlled trial. Setting: A secondary public health facility in Sydney, Australia. Participants: Seventy adults with greater than 3-month history of LBP and a directional preference. Interventions: Participants were randomized to receive 12 treatments of either the McKenzie method or motor control exercises over 8-weeks. Outcome measures: Muscle thickness of the transversus abdominis, obliquus internus, and obliquus externus measured from ultrasound images. Secondary outcomes included function, perceived recovery, and pain. Outcomes were collected at baseline, post intervention at 8-weeks, and at 1-year follow-up by blinded assessors. The current paper focuses on the 1-year follow-up. Results: Fifty-eight participants completed data collection for the primary outcome at 1-year. There were no significant between group differences for changes in trunk muscle thickness for any of the three investigated muscles: transversus abdominis [3%, 95% confidence interval (CI): ���5%, 11%], obliquus internus [���4%, 95% CI: ���9%, 2%] and obliquus externus [3%, 95% CI: ���4%, 11%]. Similarly, there were no significant differences between groups for the secondary outcomes of function, perceived recovery and pain. Conclusion: Trunk muscle thickness, function, perceive recovery and pain are similar between patients receiving McKenzie method or motor control exercises at a 1-year follow-up in a population of people with chronic LBP and a directional preference. Clinical Trials Registration number CTRN12611000971932.