Since complete excision of the fistula tract is essential in surgery for pyriform sinus, identifying the fistula tract is the key to the surgical procedure. However, the tract is often difficult to identify because of complicating infection or small size of the tract in neonatal cases. Herein, we report our experience of attempting to visualize the fistula tracts in two cases of pyriform sinus fistula. In one case, insufflation by upper gastrointestinal endoscopy was used to identify the fistula, and the fistula tract was stained with pyoktanin blue from the fistula opening. In the other case, a neotate, the tract was found as a cyst by magnetic resonance imaging. Direct injection of pyoktanin blue into the cyst enabled easy visualization of the fistula tract, and the surgery was performed successfully. These methods are considered potentially applicable to visualize the fistulous tract in cases of pyriform sinus fistula.