© TÜBİTAK.Background/aim: This study objected to compare the measurements of corpus callosum substructures of adolescents with migraine and healthy adolescents. Materials and methods: In a case-control design, adolescents aged 12–18 years with the diagnosis of migraine and healthy control group had brain magnetic resonance imaging examination. The CC dimensions including anteroposterior length, truncus, genu and splenium widths of the case and control groups were measured and compared. Results: The sample consisted of 188 adolescents, 109 girls (58.0%), and 79 boys (42.0%). Of these 87 (46.3%) were in the migraine group and 101 (53.7%) were in the healthy control group. The mean genu and splenium width of the migraine group were significantly lower than the control group (p = 0.024 and p = 0.01 respectively). Conclusion: The results of this study firstly demonstrated that CC splenium and genu widths were smaller in adolescents with migraine when compared to healthy adolescents. Our findings may contribute to enlighten migraine pathophysiology.