Immunisation is the most cost-effective public health intervention currently available. However, immunisation raises ethical conflicts as it may be considered a public good with little individual benefits. Considering the effectiveness of immunisation in controlling vaccine preventable infections and the constant threat of outbreaks from conditions like measles, refusal to participate in a universal immunisation programme is morally questionable. This research analyses the ethical issues brought up by universal immunisation in South Africa. It focuses on local practice and on selected risk benefit issues. The research method used is literature search with analysis in the form of critical thinking and moral reasoning. The findings are that universal immunisation is ethically defensible based on various ethical theories and principles. South Africa’s experience with the 2003 -2005 measles outbreak points to a social contract for individuals to immunise their children. The argument of taking personal risk for public good and the no additional benefit argument once herd immunity is reached (presented by Dawson), are refuted. Risk-benefit elements for each infectious condition and vaccine are continually changing. This demands an ongoing assessment of risk-benefit issues for each vaccine and targeted infections to ensure the use of vaccines with optimal safety levels that are appropriate in South Africa. Recommendations are made on immunisation policy and legislation aimed at improving ethical practices of the immunisation service. Implementation of the recommendations will help ensure an immunisation programme that is proactive in addressing associated risks and should help eliminate litigation. The main recommendation of a legislated Compensation System for those who suffer severe adverse events following immunisation is directed at just distribution of benefits and burdens.