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Background To estimate the effect of strabismus (squinting) on mental health and health-related quality of life aspects in children and adolescents. Methods Data from the German Health Interview and Examination Survey for Children and Adolescents KiGGS (2003–2006 baseline survey; N = 14,835, aged 3 to 17 years, 49% girls) were examined. The presence of strabismus was derived by parental questionnaire, and health-related quality of life and mental health were investigated with the KINDL-R and Strengths and Difficulties Questionnaire. Associations between strabismus and outcomes were analyzed using multivariable linear and logistic regression models. Results Of 12,989 children without missing data, 579 children (4.5% of the sample) were reported to have strabismus. Children with strabismus had lower scores in the parent-reported KINDL-R total scale (adjusted beta = − 1.02; 95%CI: -1.86 to − 0.18; p = 0.018) and sub-scale ‘friends’ (adjusted beta = − 2.18; 95%CI: -3.56 to -0.80; p = 0.002) compared to children without strabismus. The presence of strabismus was also associated with more mental health problems like ‘hyperactivity/inattention’ (adjusted OR = 1.50; 95%CI: 1.14 to 1.98; p = 0.005), and ‘peer problems’ (adjusted OR = 1.35; 95%-CI: 1.05 to 1.74; p = 0.018) as reported by parents. Conclusions Strabismus in children and adolescents is associated with lower health-related quality of life. Electronic supplementary material The online version of this article (10.1186/s12955-019-1144-7) contains supplementary material, which is available to authorized users.