Background: Patent foramen ovale (PFO) is considered to be a risk factor for ischemic cerebrovascular disease (ICVD), especially in young people. However, the potential pathophysiological relevance in ischemic stroke is controversial and in need of further investigation. In this study, we examined the conventional risk factors and the distribution of 100 polymorphisms in 47 suspected susceptibility genes for ICVD in stroke patients with or without a PFO. Methods: In the South Stockholm Ischemic Stroke Study, 928 ICVD patients and 602 controls were genotyped for 100 different gene polymorphisms. The stroke patients also underwent relevant investigation and standardized blood tests. Patients who underwent transeosophageal echocardiography as part of their investigation were divided into groups that either had or did not have a PFO. Results: There were no significant differences in the 2 groups with regard to conventional risk factors or blood analyses. Three different polymorphisms located in the prothrombin, F2 (20210G/A), and apolipoprotein-C3 (-641A/C and -455T/A) genes were significantly associated with ICVD and PFO. The strongest association was found for F2 (P = .0049; odds ratio 26.4). Conclusions: We found that F2, which previously has been described as being a possible link between PFO and ICVD, was significantly associated with ICVD and PFO. There was also a trend toward an association between 2 other polymorphisms in the APO-CIII gene and PFO and ICVD.