Objective: The study was designed to determine the risk perception of the public population in Kota Kinabalu towards childhood immunisation. Methodology: This was a cross-sectional study where self-administered questionnaires were distributed to the public in Kota Kinabalu. The respondents who consented were 18 years old and older. The illiterate persons and the foreigners were excluded. The calculated sample size was 400. Only 313 samples collected were suitable for analysis using SPSS21.0. Results: Fever, pain swelling and allergic reaction were correctly identified as risks of immunisation. Autism, mental retardation and even death could also result from vaccination. Of the total respondents, 76.7% agreed with the practice of childhood vaccination, 70.0% thought that childhood vaccinations were safe and effective and 58.1% felt that its benefit outweighed the risk. Other than that, 32.0% refused childhood vaccination from fear of its risks, and this fear was the main reason for the refusal of childhood vaccination. Age, marital status, race and income were the factors which influenced parental willingness to vaccinate their children (p<0.05). Conclusions: Most participants understood the risks of childhood vaccination, but few agreed to the practice of childhood immunisation for herd immunity. Public health campaigns are needed, to increase the understanding and acceptance of childhood vaccination especially in the rural community.