Objective To assess the changes in normal-appearing white matter fiber tracts of the brainstem in patients with relapsing-remitting multiple sclerosis (RRMS) quantitatively with diffusion tensor imaging (DTI). Methods Fifty patients with RRMS were recruited, and twenty five healthy volunteers with the same gender and age were selected as controls. Conventional magnetic resonance imaging and DTI was performed. Quantitative indexes as fractional anisotropy (FA) and mean diffusivity (MD) values in the brainstem fiber tracts, including corticopontine tract/corticospinal tract (cpt/cst), superior cerebellar peduncle (scp), middle cerebellar peduncle (mcp), inferior cerebellar peduncle (icp), and medial lemniscus (ml) were measured and analyzed. Results In comparison with controls, decreasing FA values in cpt/cst (L:P=0.030; R:P=0.020), icp (L:P=0.030; R:P=0.037), scp (L:P=0.036; R:P=0.041) and ml (L:P=0.014; R:P=0.035), as well as increasing MD values in cpt/cst (L:P=0.004; R:P=0.046), icp (L:P=0.047; R:P=0.011), scp (L:P=0.021; R:P=0.011) and ml (L:P=0.002; R:P=0.044) were found in patients with RRMS. No significant difference of FA and MD values was found in mcp between patients with RRMS and controls (P＞0.05). None of the MD or FA values in fiber tracts of the brainstem in patients with RRMS was correlated with brain parenchymal fraction (BPF) or T2 lesion volume. Conclusion The relevant abnormalities which were found in normal-appearing white matter fiber tracts of the brainstem in RRMS patients by DTI scanning suggested pathological changes. It is presumed that the changes may be due to demyelination caused by hiding lesions.