Purpose Hypothesis that loss of integrity of the membranes in the craniocervical junction might be the cause of neck pain in patients with whiplash-associated disorders (WADs) has been proposed. In recent years, with development of more detailed magnetic resonance imaging (MRI) techniques, morphologic changes of the ligaments and membranes in the craniocervical junction, especially alar and transverse ligaments have been discussed. A metaanalysis was performed to evaluate the relationship of MRI signal changes of alar and transverse ligaments and WADs. Methods A systematic search of EMBASE, PUBMED, and Cochrane Library and references from eligible articles were conducted. Comparative studies reporting on evaluating the relationship between MRI high-signal changes of alar and transverse ligaments and WADs were regarded eligible. A pooled estimate of effect size was produced. Results Alar ligaments: Six studies (total n = 622) were included. MRI signal changes of alar ligaments did not appear to be related with WADs (P = 0.20, OR = 1.54, 95 % CI = 0.80-2.94). Heterogeneity was present (I 2 = 46 %, P = 0.10), which was eliminated upon sensitivity analysis bringing the OR to 1.27 (95 % CI = 0.87-1.86, I 2 = 0 %). Transverse ligaments: Four studies (total n = 489) were included. MRI signal changes of transverse ligament did not appear to be related with WADs (P = 0.51, OR = 1.44, 95 % CI = 0.49-4.21). Heterogeneity was present (I 2 = 77 %, P = 0.005), which was eliminated upon sensitivity analysis bringing the OR to 0.79 (95 % CI = 0.49-1.28, I 2 = 0 %). Conclusion MRI signal changes of alar and transverse ligaments are not supposed to be caused by whiplash injury, and MRI examination of alar and transverse ligaments should not be used as the routine workup of patients with WADs.