Objective To investigate the role of contrast transesophageal echocardiography (cTEE) in detecting right-to-left shunt (RLS) and identifying its sources in migraine aura (MA), and to study the significance of different RLS types in the etiologies of MA. Methods 107 patients with MA and 45 were enrolled. cTEE was applied to identify whether there were RLS and their sources at rest and during Valsalva maneuver respectively, and to semi-quantitatively grade the shunts.?Results The total incidence of RLS of the patients with MA was higher than that in normal control group (69.2% versus 17.8%, P < 0.05). Besides, the ratio of patients with only PFO-RLS (patent foramen ovale right-to-left shunt, PFO-RLS), only P-RLS (intra-pulmonary right-to-left shunt, P-RLS), and both P-RLS and PFO-RLS detected in MA patients were 10.3%, 19.6%, 39.3%, which were all higher than those in control group (4.4%, 8.9%, 4.4%, all P < 0.05). Furthermore, the ratio of moderate or above RLS in MA group was significantly higher (P < 0.05) than that in healthy volunteers. Conclusion Both P-RLS and PFO-RLS have significant roles in etiologies of MA. cTEE is an objective and effective method for the diagnosis, differentiation, and quantitative analysis of RLS.