Background: To estimate the prevalence of strabismus and associated risk factors among grade one school children in Lhasa, Tibet, China. Methods: The Lhasa Childhood Eye Study (LCES) was a cross-sectional, school-based childhood study conducted in Grade one students from primary schools in Lhasa, Tibet, China. Comprehensive ophthalmic examinations and basic systemic examinations were evaluated. A questionnaire survey containing information about children, as well as parents' information, was sent to the corresponding parents of eligible children. The prevalence of strabismus and its 95% confidence interval was estimated. Univariate and multivariate logistic regression analyses were conducted to determine the associated risk factors. Results: A total of 1942 eligible grade one students were enrolled, of which 1856 participants completed all examinations. The average age was 6.83 +/- 0.46 years, 53% of participants were boys and 1762 were the Tibetan Minority. Over all, the prevalence of strabismus was 68/1856 (3.7%) (95%CI: 2.81,4.52), with no difference between the ages, genders, ethnicities and body mass index, while tilting one's head when writing may be a risk factor for strabismus (P = 0.004). Strabismus students had mean best corrected visual acuity of 0.16 +/- 0.28(LogMAR), over 50% patients with esotropia were hyperopic, and participants who had stereopsis impairments showed a significant difference between esotropia and exotropia (P = 0.026). Conclusions: The prevalence of strabismus in LCES was 3.7%, which is higher than previous reports from Chinese childhood epidemiology studies. Strabismus is a common contributing factor to amblyopia. Tilting one's head when writing may be a risk factor. Esotropia is more likely to affect stereopsis and be associated with the refractive state of hyperopia.