Vaccine hesitancy is considered to be a threat to the success of vaccination program and control of infectious diseases. It affects the morbidity and mortality thus overwhelms the health care system. Up to our knowledge there is no formal study done to assess vaccine hesitancy in Bahrain. The aim and objectives of this study is to determine the prevalence of vaccine hesitancy towards childhood vaccination in Kingdom of Bahrain. A cross sectional study was conducted in Bahrain’s five health regions. One primary health care center was selected randomly from each health region. Participants were systematically selected; every third attendant was asked to fill a self-administer PACV questionnaire. A total of 707 participants were enrolled in the study. This study found that 5.8% of participants were hesitant to vaccinate their children. Non-Bahraini were found to be more hesitant than Bahraini. In addition, 33.3% of the hesitant participants delayed their child's vaccination and 38.2% decided not to have their child vaccinated for reasons other than illness or allergy. Most of the hesitant participants had concerns about vaccine safety, as 65.9% of the hesitant participants were concerned that the child might have a serious side effect from the vaccine, 63.4% were concerned that childhood vaccines might not be safe and more than two third of them preferred that their children get fewer vaccines at the same time. However, 45.9% of the hesitant participants have trust issues about their child’s doctor. Although Kingdom of Bahrain has a high immunization coverage and low prevalence of hesitancy towards childhood’s vaccines, addressing vaccine hesitancy is important to maintain the high vaccination coverage and prevent communicable diseases targeted by vaccination.