Abstract Background Manual spinal joint mobilisations and manipulations are widely used treatments in patients with neck and low-back pain. Inter-examiner reliability of passive intervertebral motion assessment of the cervical and lumbar spine, perceived as important for indicating these interventions, is poor within a univariable approach. The diagnostic process as a whole in daily practice in manual therapy has a multivariable character, however, in which the use and interpretation of passive intervertebral motion assessment depend on earlier results from the diagnostic process. To date, the inter-examiner reliability among manual therapists of a multivariable diagnostic decision-making process in patients with neck or low-back pain is unknown. Methods This study will be conducted as a repeated-measures design in which 14 pairs of manual therapists independently examine a consecutive series of a planned total of 165 patients with neck or low-back pain presenting in primary care physiotherapy. Primary outcome measure is therapists’ decision about whether or not manual spinal joint mobilisations or manipulations, or both, are indicated in each patient, alone or as part of a multimodal treatment. Therapists will largely be free to conduct the full diagnostic process based on their formulated examination objectives. For each pair of therapists, 2×2 tables will be constructed and reliability for the dichotomous decision will be expressed using Cohen’s kappa. In addition, observed agreement, prevalence of positive decisions, prevalence index, bias index, and specific agreement in positive and negative decisions will be calculated. Univariable logistic regression analysis of concordant decisions will be performed to explore which demographic, professional, or clinical factors contributed to reliability. Discussion This study will provide an estimate of the inter-examiner reliability among manual therapists of indicating spinal joint mobilisations or manipulations in patients with neck or low-back pain based on a multivariable diagnostic reasoning and decision-making process, as opposed to reliability of individual tests. As such, it is proposed as an initial step toward the development of an alternative approach to current classification systems and prediction rules for identifying those patients with spinal disorders that may show a better response to manual therapy which can be incorporated in randomised clinical trials. Potential methodological limitations of this study are discussed.