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Background: Chronic nonspecific low back pain (CNLBP) is among the most prevalent health problems. Lumbar spine and hips kinematics and coordination can be affected in CNLBP. The effects of exercises on the kinematics and coordination of lumbar spine and hips during sit-to-stand (STS) and its reverse have not been evaluated. Objective: The aim of this study is to investigate the effect of core stabilization exercise on the kinematics and joint coordination of the lumbar spine and hip during STS and its reverse in CNLBP patients. Methods: COSCIOUS is a parallel randomized double-blind controlled trial. A total of 30 CNLBP patients and 15 asymptomatic participants will be included. The kinematics and joint coordination of the lumbar spine and hips will be evaluated during STS and its reverse using a motion capture system. The participants will be asked to sit in their usual posture on a stool. Reflective markers will be placed over the T12, S2, anterior and posterior superior iliac spines, greater trochanters, and lateral femoral epicondyles of both legs. The participants will be instructed to stand up at natural speed, remain in the erect posture for 3 seconds, and then sit down. Kinematic variables of the lumbar spine and hip will be computed. Afterward, the CNLBP participants will be allocated at random to receive one of 2 interventions: core stabilization or general exercise. Treatment sessions will be held 3 times per week for 16 sessions. After intervention, CNLBP participants will be assessed again. Results: Funding for the study was provided in 2016 by Iran University of Medical Sciences. The study is expected to last approximately 12 months, depending on recruitment. Findings on the study’s primary outcomes are expected to be finalized by December 2017. The results of the study will be published in a peer-reviewed journal. Conclusions: This investigation will evaluate the effects of core stabilization exercise on the kinematics and joint coordination of the lumbar spine and hip during STS and its reverse in patients with CNLBP. In addition, the effects of CNLBP on STS and its reverse will be investigated in COSCIOUS. Trial Registration: Iranian Registry of Clinical Trials IRCT2016080812953N2; http://en.search.irct.ir/view/32003?format=xml (Archived by WebCite at http://www.webcitation.org/6qjTWd4Az) [JMIR Res Protoc 2017;6(6):e109]