Background: Intra-operative pulmonary embolism (PE) is a rare but fatal complication leading to sudden intra-operative cardiovascular collapse with most cases being diagnosed by post mortem. Accurate diagnosis is often difficult as other more common causes of cardiovascular collapse are considered. Real time Transesophageal Echocardiography (TEE) in addition to commonly used intra-operative anesthesia monitoring is a key modality in aiding immediate diagnosis allowing for the appropriate critical care. Case Report: We report an unusual case of intra-operative PE during elective laparoscopic colectomy in a patient suffering from Crohn's colitis, diagnosed by intra-operative TEE. Post-operative CT pulmonary angiogram confirmed the diagnosis. Intensive supportive treatment led to regaining hemodynamic stability and was followed by complete recovery. Conclusion: This case report is unique in several aspects which will be discussed, but most importantly should raise awareness amongst all care givers of inflammatory bowel disease patients who undergo major surgery after prolonged pre-operative hospitalization with increased risk of thrombo-embolic complications.