Background Gynecomastia is benign enlargement of breast tissue in males and is fairly common. Mastectomy not only helps in improving the shape of anterior chest, but can also improve the location of nipple. Therefore, a principle element of mastectomy design is defining the normal location of nipple based on major anatomical reference points. Here, the nipple location was compared for before and after gynecomastia surgery. In addition, the same was also compared between male patients undergoing gynecomastia surgery and control group of subjects without gynecomastia. Methods We retrospectively analyzed gynecomastia patients who underwent conventional subcutaneous mastectomy. Preoperative and postoperative anatomical landmark distances and chest circumferences were measured and compared to the same anthropometric data from 20 healthy adult male controls. Results Nipple locations were compared among 13 patients and 20 controls. The mean weight of resected breast tissue was 246 g, and overall patient satisfaction grade was 4.3 out of 5. In the patient group, the slopes for the height-distance from the sternal notch to the nipple and chest circumference-distance between the mid-line of the sternum and the nipple were 0.175 and 0.125 postoperatively, respectively. The slopes of the control group were 0.122 and 0.177, respectively; these differences were statistically significant (P<0.05). Conclusions Nipple positions were considerably lower in patients with gynecomastia than in control subjects. Subcutaneous mastectomy was associated with mild elevations, but postoperative locations were still lower compared to controls. Further efforts are needed to improve the location of postoperative nipple-areola complex in patients with gynecomastia.