High-resolution optical coherence tomography can detect in situ thrombi within patent foramen ovale (PFO), which can become a dangerous embolic source. This study aimed to investigate the frequency and size of in situ thrombus within PFO using optical coherence tomography.The cross-sectional study was conducted at Fuwai Hospital (Beijing, China) between 2020 and 2021. From 528 consecutive patients with PFO, 117 (age, 34.33 [SD, 11.30] years) without known vascular risk factors were included; according to PFO-related symptoms, they were divided into the stroke (n=43, including 5 patients with transient ischemic attack), migraine (n=49) and asymptomatic (n=25) groups. Optical coherence tomography was used to evaluate in situ thrombi and abnormal endocardium within PFO. Univariable analysis and a logistic model were used to evaluate the association between stroke and in situ thrombus; age, sex, body mass index, and antithrombotic therapy were included as covariates.Antithrombotic therapy was used more frequently in the stroke group than in the migraine group (76.7% versus 12.2%; P<0.001). In situ PFO thrombi were detected in 36 (83.7%), 28 (57.1%), and 0 (0.0%) patients from the stroke, migraine, and asymptomatic groups, respectively (P<0.001). Between the stroke and migraine groups, there was no significant difference in the median (interquartile range) thrombus number per patient (7 [3-12] versus 2 [0-10]; P=0.199), maximum thrombus diameter (0.35 [0.20-0.46] versus 0.21 [0-0.68] mm; P=0.597), or total thrombus volume (0.02 [0.01-0.05] versus 0.01 [0-0.05] mm3; P=0.386). Additionally, in situ thrombus was significantly associated with stroke risk (odds ratio, 4.59 [95% CI, 1.26-16.69]). Abnormal endocardium within PFO occurred in patients with in situ thrombi (71.9%) but not in those without. During optical coherence tomography examination, migraine occurred in 2 patients with in situ thrombi.The frequency of in situ thrombus was extremely high in stroke and migraine groups, while none of the asymptomatic individuals presented with an in situ thrombus. In situ thrombus formation may play a role in patients with PFO-associated stroke or migraines and have therapeutic implications.URL: https://www.gov; Unique identifier: NCT04686253.