Branch pulmonary artery obstruction is one of the prime reasons for re-operation in patients who have undergone repair for tetralogy of Fallot. Branch pulmonary artery obstruction may develop over a period of time due to dilation of right ventricular outflow tract or it may be caused by residual stenosis after inadequate repair. This may lead to differential lung perfusion causing morbidity. Intra-operative capnogram monitoring reveals ventilation-perfusion relationship. We report two cases where the capnogram helped the diagnosis and management of branch pulmonary artery obstruction. We found a redundant patch in the first and an extra length of the homograft in second case which led to the obstruction. However, but for the changes in the intraoperative capnogram, this condition may by far remain undiagnosed considering the fact that it does not produce hemodynamic changes but can lead to postoperative morbidity.