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This study compared the relationship between some clinical factors and the size of neck flexors in participants with or without chronic neck pain.In this case-control study, the correlation between flexor endurance capacity as well as thickness, cross-section area, and shape ratio of longus colli/capitis and sternocleidomastoid muscles were examined in 30 patients with chronic neck pain and 30 asymptomatic participants.The patients showed lower flexor endurance (P = 0.02), smaller thickness (P = 0.03), and cross-section area (P < 0.01) of longus colli as compared with controls. Longus capitis and sternocleidomastoid size were not different between the two groups. The flexor endurance showed a negative correlation with longus colli shape ratio (r = −0.38, P = 0.03) and a positive correlation with longus capitis cross-section area (r = 0.38, P = 0.03) in the patients with chronic neck pain. In the control group, flexor endurance was negatively correlated with longus colli shape ratio (r = −0.45, P = 0.01) but positively correlated with longus capitis thickness (r = 0.45, P = 0.01) and cross-section area (r = 0.38, P = 0.03). Neck disability and pain intensity indices were not significantly correlated with either flexor muscles endurance or size.The ultrasonographic measures of the deep neck flexor muscles and the flexor endurance test, being associated with each other, could successfully differentiate patients with chronic neck pain from asymptomatic participants. However, the endurance test scores were not correlated with self-reported disability or pain intensity indices.