In patients who undergo median sternotomy to treat congenital heart diseases, a thymectomy is performed to yield better access to the cardiac system. In this study we have used MRI to evaluate the changes in size, shape and location of the thymus after midsternatomy. This case-control study was performed during 2011-2012 in Shiraz, Iran. Eligible participants between 5-17 years of age were divided into case and control groups (n=13 per group). Each participant underwent a median sternotomy at least one year prior to study entry. Participants were initially examined by a cardiologist and then referred for MRI. A radiologist examined all MRI images. The thymus was observed in all control group patients and in only 7 (53.8%) patients in the case group. There was a significant relationship noted in terms of mean age in the group whose thymus was visible and the group in which the thymus was not visible. We have observed no significant difference in thymic visibility between these two groups based on the mean age at midsternatomy. In pediatric patients undergoing cardiac surgery the possibility of remaining or regenerated thymic tissues may be evaluated by MRI. The remaining portion of the thymus may have any shape, size or location. Therefore, it can be misinterpreted as a mass if a patient’s previous surgical history and age at the time of surgery are not taken into consideration.