Introduction: Vaccination is a biological process that improves immunity level of an individual towards certain diseases. Vaccination is generally given to all newborn and kids. Most countries oblige their citizens to be vaccinated as early as new-born age. The aim of this research is to study the perception on vaccination intake and the associated factors that lead to its refusal among parents in east coast and west coast peninsular Malaysia. Methods: Primary data were collected using self-administered questionnaire and were distributed to assess the study objectives. Total 240 questionnaires were distributed equally in west coast and east coast study area. Questionnaire consists of demographic data, perception aspects and factors that may lead to the negative perceptions. Results: There is significant association between perception and religion, education level and side effect factor in east coast with majority of the respondents are Muslims (40.83%) while there is no significant association between education level and side effect factor (p>0.1) in west coast with majority of respondents are Muslims (51.67%) too. This study found that perception regarding vaccination is influenced by the religion restrictions in east coast of peninsular Malaysia and not in west coast region. The other factors associated with vaccination refusal varies according to education level, and regional basis. Conclusion: Most of the respondents who have negative perception regarding vaccination are from East Coast region as they are more prone into Islamic teachings. All the possible factors of vaccination refusal are accepted by the respondents but varies in its prevalence as the leading factor determined that caused the vaccination refusal are religion restriction and the least percentage for the factor is time restriction.