Cerebral embolization through a PFO is considered to be a possible cause of migraine attack, therefore the size of the PFO and its 'functional potential' should play an important etiological role in migraine. However, this relationship remains complex due to various methodological issues. We have highlighted some of the important issues related to the diagnostic methodology for PFO and the interpretation of the results. Mere detection of the presence of PFO in patients with migraine may not delineate their true relationship for a better understanding and planning a definitive treatment. There is an urgent need for standardizing the diagnostic methods as well as the criteria for the grading the 'functional status' of PFO.