To investigate the potential factors related to variability of alignment in childhood concomitant strabismus.Prospective inter-examiner (test-retest) reliability analysis.In total, 197 children with concomitant strabismus (57 esotropia, 140 exotropia) underwent repeat prism and alternate cover test (PACT) by two orthoptists who were certified by the study, and sensory tests were all performed once. We defined the alignment measurement as stable if the absolute value of the measurement difference between two orthoptists was within 10 prism diopters (PD), and unstable if the difference was 10 PD or greater. We analyzed the relationship between the measurement variability and sensory results, patient age, and angle of deviations.The mean age of the esotropia and exotropia patients was 68.5 ± 26.3 months (range, 36-164 months) and 96.0 ± 33.7 months (range, 22-200 months), respectively, and there was a significant difference in suppression related variability of alignment, both at distance (P = 0.004) and at near (P = 0.046). Anisometropia also showed a significant difference at distance (P = 0.035) for variability of alignment, and there was no significant statistical effect of age on measurement variability in our study. Variability of alignment is positively associated with the angle of deviation, especially at distance (P = 0.021 for exotropia, P = 0.002 for esotropia) with more variability between observers with larger angles of misalignment.Suppression is an important factor for variability of alignment in childhood concomitant strabismus. Other factors, such as anisometropia and a large angle of strabismus should be taken into account when evaluating binocular alignment.Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.