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Background: Hesitancy towards vaccination has been studied as a barrier to vaccination among children, as well as participation in vaccine trials. This study aimed to investigate hesitancy towards vaccination among parents in Indonesia, as a part of the Indonesia Zika Vaccine Study. Methods: A cross-sectional study was conducted in eleven regencies and municipalities in Aceh and West Sumatra province, Indonesia. Parents were recruited from families at outpatient clinics of community health centers or hospitals. The survey included various questions about sociodemographic factors and the Parent Attitudes about Childhood Vaccination (PACV) scale. Linear regression was employed to assess the association between explanatory variables and vaccine hesitancy. Results: A total of 956 parents were interviewed and 26.4% of participants had heard about Zika. Overall, 152 parents (15.9%) were vaccine hesitant, and this proportion was the highest in the safety and efficacy subdomain (61.6%). In the unadjusted analysis, having a diploma certificate, working in the health sector, and having heard about Zika were significantly associated with non-hesitancy towards children vaccination. Having heard about Zika was the only factor that was significantly associated with hesitancy towards vaccination in multivariate model (aOR: 0.43, 95% CI: 0.26-0.71). Mothers, younger parents (aged 20-29 years old), and those with only a primary school education were more concerned about vaccine safety and efficacy compared to fathers, older groups, and individuals with more education, respectively. Conclusions: Hesitancy towards pediatric vaccination is observed in 15% of respondents and most of the hesitancy was expressed in terms of vaccine safety and efficacy. Therefore, continuous dissemination of vaccine information needs to be carried out to earn parents' trust and increase vaccination coverage in Indonesia.