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Background: Chronic low back pain is an expensive and difficult condition to treat. One of the interventions widely used by physiotherapists in the treatment of chronic non-specific low back pain is exercise therapy based upon the Pilates principles. Pilates exercises can be performed with or without specific equipment. These two types of Pilates exercises have never been compared on a high-quality randomised controlled trial. Methods/design: This randomised controlled trial with a blinded assessor will evaluate eighty six patients of both genders with chronic low back pain, aged between 18 and 60 years, from one Brazilian private physiotherapy clinic. The patients will be randomly allocated into two groups: Mat Group will perform the exercises on the ground while the Equipment-based Group will perform the Pilates method exercises on the following equipment: Cadillac, Reformer, Ladder Barrel, and Step Chair. The general and specific disability of the patient, kinesiophobia, pain intensity and global perceived effect will be evaluated by a blinded assessor before randomisation and at six weeks and six months after randomisation. In addition, the expectation of the participants and their confidence with the treatment will be evaluated before randomisation and after the first treatment session, respectively. Discussion: This will be the first study aiming to compare the effectiveness of Mat and Equipment-based Pilates exercises in patients with chronic non-specific low back pain. The results may help health-care professionals in clinical decision-making and could potentially reduce the treatment costs of this condition. [ABSTRACT FROM AUTHOR]