Persistent (patent) foramen ovale (PFO) is a recognized risk for decompression sickness (DCS) in divers, which may be mitigated by conservative diving or by PFO closure. Our study aimed to compare the effectiveness of these two risk mitigation interventions. This was a prospective study on divers who tested positive for PFO or an atrial septal defect (ASD) and either decided to continue diving without closure ('conservative group'), or to close their PFO/ASD and continue diving ('closure group'). Divers' characteristics, medical history, history of diving and history of DCS were reported at enrollment and annually after that. The outcome measures were the incidence rate of DCS, frequency and intensity of diving activities, and adverse events of closure. Divers in both groups dived less and had a lower incidence rate of confirmed DCS than before the intervention. In the closure group (n = 42) the incidence rate of confirmed DCS decreased significantly. Divers with a large PFO experienced the greatest reduction in total DCS. In the conservative group (n = 23), the post-intervention decrease in confirmed DCS incidence rate was not significant. Of note, not all divers returned to diving after closure. Seven subjects reported mild adverse events associated with closure; one subject reported a serious adverse event. PFO closure should be considered on an individual basis. In particular, individuals who are healthy, have a significant DCS burden, a large PFO or seek to pursue advanced diving may benefit from closure.