More than half of the bipolar depression (BD) subjects are misdiagnosed as unipolar depression (UD) due to lack of objective diagnostic criteria. We aimed to identify microstructural neuronal changes differentiating BD from UD groups using diffusion kurtosis imaging (DKI). The objective of the study is to identify an objective neuro-imaging marker to differentiate BD from UD. A prospective, cross-sectional study included total of 62 subjects with diagnosis of bipolar depression (n = 21), unipolar depression (n = 21), and healthy controls (n = 20). All subjects underwent diffusion-weighted imaging (b = 0,1000,2000) of the whole brain on 3-Tesla MR scanner. DKI data was analyzed using 189 region whole-brain atlas. Eight diffusion and kurtosis metrics including mean diffusivity (MD), axial diffusivity (AD), radial diffusivity (RD), fractional anisotropy (FA), mean kurtosis (MK), axial kurtosis (AK), radial kurtosis (RK), and kurtosis fractional anisotropy (FKA) were measured against these 189 regions. Principle component analysis (PCA) was utilized to identify the most significant regions of the brain. ANOVA with post hoc tests was used for analyzing these regions. BD group showed increased MD, RD, decreased AK at the left amygdala and decreased MK and RK at the right hemi-cerebellum. UD group showed increased MK and RK at the right external capsule; and increased AK, MK, and RK at the right amygdala. The right and left amygdala, right external capsule, and right hemi-cerebellum showed microstructural abnormalities capable of differentiating BD and UD groups. Diffusion imaging especially DKI can aid in management of depression patients.