Objective: To compare the effects of an isolated application of cervical spine thrust joint manipulation vs. the application of cervical, cervico-thoracic junction and thoracic manipulation on neck pain, disability and cervical range of motion in chronic neck pain. Design: Randomized clinical trial. Setting: Clinical practice. Participants: Eighty-two patients (41 females) with chronic mechanical neck pain. Interventions: Patients were randomly assigned to a cervical spine manipulation group or a full manipulative group who received mid-cervical, cervico-thoracic and thoracic joint manipulations. Measurements: Neck pain intensity (11-point numeric pain rating scale), self-reported disability (Neck Disability Index) and cervical range of motion were collected at baseline and one week after the intervention by an assessor blinded to the allocation of the patients. Results: A significant Group * Time interaction for Neck Disability Index (P = 0.022), but not for neck pain (P = 0.612), was found: patients in the full manipulative group exhibited greater reduction in disability than those who received the cervical spine manipulation alone, whereas both groups experienced similar decreases in neck pain. Patients in both groups experienced similar increases in cervical range of motion (P > 0.4). No effect of gender was observed (P > 0.299). Conclusions: In patients with chronic mechanical neck pain, manipulation of the cervical and thoracic spine leads to a greater reduction in disability at one week than after manipulation of the cervical spine alone, whereas changes in pain and range of motion are not affected differently.