The Croatian Immunization Programme is a mandatory prevention programme in which vaccines are offered free of charge and little is known about parental vaccine-related beliefs and attitudes. We aimed to describe beliefs and attitudes towards childhood vaccination of parents in Zagreb, estimate the proportion of parents with positive attitudes towards vaccination, and to identify the possible predictors of positive attitudes. Using a self- administered questionnaire, we performed a cluster sampling survey among parents of 6-years- old children in Zagreb. In total 542 questionnaires were collected, 80% (n = 430/542) of respondents were mothers. Even though 72.6% (n = 385/531 ; 95%CI: 69–76) respondents feel that childhood vaccination should remain mandatory, 36.3% (n = 192/528 ; 95%CI: 58.3–65.3) considered that simultaneous administration of vaccines can have negative effect to their child’s health. In addition, 38% (n = 202/532 ; 95%CI: 33.2–43.1%) feared that vaccines may harm their child. Of total, parents mostly reported positive attitude towards vaccination (61.8% ; 95% CI: 34.7–42). Parents with positive attitudes were more likely to state their child experienced mild or no adverse reaction after vaccination, report not delaying vaccination and provide additional non- mandatory vaccines to their child (p < 0.05). Gender, age, education and marital status of parent were not significantly associated with the positive attitude towards vaccination. Our results suggest the need for educational interventions and communication strategies that could foster better knowledge on immunization with a focus on parental misconceptions, perceived constraints and safety issues about vaccine.