Methods, devices and systems for treating patent foramen ovale (PFO) involve advancing a catheter device to a position in a heart for treating a PFO, bringing tissues adjacent the PFO at least partially together, and applying energy to the tissues to substantially close the PFO acutely. Catheter devices generally include an elongate catheter body, at least one tissue apposition member at or near the distal end for bringing the tissues together, and at least one energy transmission member at or near the distal end for applying energy to the tissues. In some embodiments, the tissue apposition member(s) also act as the energy transmission member(s). Applied energy may be monoploar or bipolar radiofrequency energy or any other suitable energy, such as laser, microwave, ultrasound, resistive heating or the like.