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Introduction: Previous studies have reported a high prevalence of visual defects in children with special needs. However, routine ocular examinations for these children in rural areas of China are lacking. This study aimed to evaluate the status of visual impairment (VI) in children at special education schools in rural China. Methods: A total of 316 students from two special schools in Zunyi city, Guizhou province, were enrolled. Full ophthalmic examinations were performed, and gene-sequencing services were offered to potential patients. Results: The mean age of the 316 participants was 12.27 ± 3.49 years and 75 showed abnormal ophthalmic manifestations on slit-lamp examination. Visual acuity (VA) was assessed in 232 eyes, and the mean VA (logarithm of the minimum angle of resolution, logMAR) was 0.27 ± 0.34. Whole-exome sequencing identified 19 mutations in these children, which might explain their visual complaints. Children with Down syndrome had a significantly higher prevalence of ocular disorders than those without. Conclusion: VI is common among children at special education schools in rural areas; however, routine screening and effective interventions have not been consistently implemented. Efforts should be made to address this issue in these already disadvantaged children. [ABSTRACT FROM AUTHOR]