Objective: We aimed to compare magnetic resonance imaging (MRI) and atlas measurements to determine the target coordinates of globus pallidusinternus (GPi) and subthalamic nucleus (STN) during stereotactic neurosurgery. Methods: Eleven patients treated with bilateral deep brain stimulation (DBS) GPi and STN for the treatment of Parkinson’s disease (PD) were includedin the study. The target was chosen by direct visual recognition of GPi and STN in three-dimensional MRI. The coordinates were automaticallysaved using special software and converted to the anterior commissure-posterior commissure (AC-PC) coordinate system using a matrix conversionprocess. The same GPi and STN targets were identified based on the locations of brain structures shown in the Schaltenbrand atlases. MRI-based GPiand STN target coordinates were statistically compared with the corresponding atlas-based coordinates. Results: Eleven patients were included in our study. The median age was 66.6±11.72 in the GPi group and 47.50±14.20 in the STN group. The averagelength of the AC-PC line was 26.15±1.42 in the STN group; and 26.46±1.34 in the GPi group. It was quite similar in both groups for each coordinatemeasurement, and the Intra-class Correlation Coefficients of each measurement were over 90%. Conclusion: According to the results of our study, target coordinates obtained by direct visual targeting on MRI and target coordinates obtained byindirect targeting based on atlas were highly compatible. The coordinates used for DBS in the treatment of PD were confirmed by both methods.