When patent foramen ovale (PFO) combines with the prominent Eustachian valve or Chiari network (EV/CN), contrast transthoracic echocardiography (cTTE) may miss the diagnosis of PFO. We sought to determine the characteristics of right-to-left shunt (RLS) in PFO patients with prominent EV/CN on cTTE and identify the causal factors of missed diagnosis. We consecutively enrolled 98 patients who suffered from PFO-related stroke and with prominent EV/CN. All patients were divided into the delayed and non-delayed groups according to the characteristics of RLS on cTTE. The characteristics of RLS were compared with those of 42 intrapulmonary shunt patients. The anatomical characteristics of PFO and EV/CN were analyzed in the 98 PFO patients. Upon cTTE, significantly delayed occurrence and longer duration of the RLS in the delayed group were found both at rest and during the Valsalva maneuver, similar to the intrapulmonary shunt. Multivariate logistic analysis revealed that the length of EV/CN (>19 mm) and the diameter of PFO at the left atrium aspect (<1.2 mm) were high-risk factors for missed diagnosis. In conclusion, RLS showed delayed emergence and disappearance in some of the PFO patients with prominent EV/CN. The length of EV/CN and the diameter of PFO may have been related to the missed diagnosis of PFO.