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Purpose: To establish an appropriate clinical protocol for early photoscreening in 12-to-24-month-old children at pediatric well-baby clinics. Methods: This prospective study included a total of 277 children aged 12–24 months who visited a pediatric well-baby clinic. All participants underwent: 1) inquiry of medical history; 2) photoscreening with PlusoptiX A12; and 3) comprehensive ophthalmologic examinations. The optimal referral cut-off point for PlusoptiX was determined by receiver operating characteristic analyses. A high-risk subgroup was defined as having a birth weight <3000 g or a history of major systemic diseases, based on the results of multivariable risk factor analysis from children's medical history. A strategy of selective photoscreening focusing on the high-risk subgroup was evaluated. The main outcome measures included sensitivity, specificity, and positive and negative predictive values. Results: The prevalence of amblyopia risk factors in our study population was 12.3%. A total of 172 children (62.1%) were assigned to the high-risk subgroup. Compared with the nonselective photoscreening of all 277 children, selective photoscreening of the high-risk children yielded a higher positive predictive value (59.6% vs. 46.7%, p = 0.001) while showing no difference in sensitivity (82.3% vs. 85.3%, p = 0.32), specificity (92.2% vs, 86.4%, p = 0.05), and negative predictive value (97.4% vs. 97.6%, p = 0.50). Conclusion: At pediatric well-baby clinics, selective photoscreening among 12-to-24-month-old children with a birth weight <3000 g or a history of major systemic diseases helped reducing the number of children need to be screened and conserving medical resources yet identifying children at risk for timely eye care.