Protein C deficiency increases the risk of an individual to develop thromboembolism and its complications. Clinical presentation of the complication of thrombosis in an unusual site may becloud clinical judgment resulting in missed diagnosis. We present an unusual case of protein C deficiency presenting with symptoms referable to the gastrointestinal system. A 34-year-old male with recurrent abdominal discomfort and bloating, managed as a case of gastro-oesophageal reflux disease with poor clinical outcome. Physical examination was unremarkable. Upper gastrointestinal endoscopy showed varices. Abdominal ultrasound scan and CT scan of the abdomen revealed thrombus in the portal vein. Functional assays of protein C and S revealed reduce protein C activity at 65 % (70 - 140%). This case emphasizes the need for extensive investigations in patients with common, sometimes neglected abdominal symptom such as bloating. It has also contributed in expanding the differential diagnosis of bloating and manifestations of protein C deficiency.