To explore the handedness effects on phase asymmetries in deep gray matter of healthy adults by using magnetic susceptibility-weighted imaging (SWI) phase. Thirty left-handed (16 men, 14 women; age range, 20 to 57 years) and 30 age- and sex-matched right-handed (16 men, 14 women; age range, 20 to 58 years) healthy adults were examined at 3.0 T MRI. For each subject, phase values were detected in bilateral frontal white matters (FWM), caudate nucleus (CA), putamen (PU), globus pallidus (GP), thalamus (TH), red nucleus (RN) and substantia nigra (SN) on phase images. Statistical analysis was performed with paired-samples t-test and independent-samples t-test. In both handedness groups, the corrected phase values in the left hemisphere were significantly lower than those in the right one in FWM, CA, PU, GP (P < 0.05) and there was no significant hemispheric asymmetry in TH, RN and SN (P > 0.05). Differences in corrected phase values in corresponding brain regions of the same hemisphere between left-handed and right-handed groups were not statistically significant (P > 0.05). Hemispheric asymmetry of SWI phase in deep gray matter may not associate with handedness in adult brain.