Perioperative pulmonary thromboembolism during cardiac surgery is extremely rare. We report a 55-year-old male, who developed acute pulmonary thromboembolism during mitral valve repair. Intra-operative trans oesophageal echocardiography failed to demonstrate thromboembolus in the pulmonary arteries but it showed the secondary signs of acute pulmonary artery obstruction. Thromboembolectomy was done after high index of suspicion on clinical grounds was found and the patient recovered. The diagnostic accuracy and sensitivity of transoesophageal echocardiography in circumstances with altered haemodynamics is questionable and has not been investigated. Therefore, indirect evidence of pulmonary artery obstruction on echocardiography may have a predictive value and failure to demonstrate pulmonary thromboembolism by this tool should not exclude the possibility of it especially when it is highly suspected.