Although about 30% of patients with mild traumatic brain injury (mTBI) suffer prolonged symptoms after injury1, conventional anatomic magnetic resonance imaging (MRI) has not proven useful in diagnosing or predicting outcomes after mTBI. In this work we evaluated a novel technique, diffusion compartment imaging (DCI), with a mouse model of mTBI that enables study of mTBI under controlled conditions. We compared DCI and diffusion tensor imaging (DTI) changes to histopathological observations in two injury conditions (with and without persistent functional deficits). Our results suggest that, unlike DTI, DCI detects specific evidence of traumatic axonal injury. Moreover, DCI detects changes only in mice with persistent functional deficits.