Objective: To investigate the incidence, spontaneous clearance, persistence and risk factors of Blastocystis infection in a rural community in Thailand. Methods: In February 2016, a cohort study was conducted in a rural community of Thailand. Baseline information of intestinal parasitic infections and follow-up visits were conducted. Blastocystis infection was detected in stool samples examined with short-term in vitro cultivation using Jones' medium supplemented with 10% horse serum. Participants were tested for Blastocystis infection at every study visit. Cox proportional hazard regression analysis was used to evaluate co-variates to determine the incidence of Blastocystis infection. Results: Of 733 enrolled participants, 57 (7.78%) were positive and 676 (92.22%) were negative for Blastocystis infection. All 676 participants were followed-up for Blastocystis infection between December 2016 and January 2018. In all, 52 of 482 cases (10.79%) comprised individual Blastocystis infection. The incidence density rates of Blastocystis infection, of spontaneous clearance of the disease and of persistent infection were 8.13, 63.14 and 38.70 per 1 000 person-months of follow-up, respectively. Our multivariate analysis revealed that opened defecation in fields or bushes (HR=4.8; 95% CI =2.1-10.4, P <0.001), raising cows (HR=2.8; 95% CI =1.1-7.1, P =0.032), not washing hands after animal contact (HR=2.1; 95% CI =1.0-4.2, P =0.044) and presenting symptoms of nausea or vomiting (HR=2.3; 95% C/=1.0-5.3, P =0.047) were predictive associated risks for the incidence of Blastocystis infection. Conclusions: Our study indicates that the best way to prevent Blastocystis infection can be by maintaining good personal hygiene, hand washing after animal contact and improving sanitary facilities.