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The objectives of this study were to evaluate parental confidence and attitudes towards immunization in urban Guatemala between private versus public health systems and their impact on vaccination timeliness in their children. A cross-sectional survey was conducted in parents 6–18-month-old children who attended well-child outpatient clinics from two health systems (public employee-based insurance and private health care) in Guatemala City from November 2017 through August 2018. Parental demographics, household characteristics, food insecurity, vaccine hesitancy using the WHO SAGE Vaccine Hesitancy Scale, and information on parental use of social media platforms and vaccine information sources were collected. Five hundred-three parents were surveyed, most of them mothers. Only 9 parents reported they had previously refused a vaccine for their child: 8 (3.2 %) from private clinics and 1 (0.4 %) from the public clinic (p = 0.02). Significantly more children attending private clinics (226, 90.4 %) were shown to have a delay in any of their vaccines scheduled for the first 2 years of life compared to those in the public clinic (169, 66.8 %; p < 0.01). Children of parents having a college degree (84.5 vs 70.1 %; p < 0.001), earning more than US$ 1,000 per month (81.5 vs 70.7 %; p < 0.001), and having a computer at home (81.4 vs 70.2; p = 0.007) were more likely to have any delays in the scheduled vaccines. Parents seeking care at private clinics were 1.14 times more at risk of delaying a vaccine compared to those at the public clinic, adjusted for other covariates (p = 0.03, 95 % CI: 1.01, 1.28). In Guatemala, children receiving immunizations at private clinics were significantly more likely than those attending public clinics to be delayed in their immunization schedule and to remain more days without the recommended protection, especially for third doses of the primary vaccine series. [ABSTRACT FROM AUTHOR]