Two fundamental questions regarding the long-term safety of immunisation options will be investigated. Homoeoprophylaxis is nontoxic, but does the use of a long-term programme disturb the subtle bodies? Vaccination is potentially toxic and short-term adverse events are documented, but has the long-term safety of vaccination been adequately quantified? The long-term energetic effects of homoeoprophylaxis programmes have not been extensively studied. One identified English-language study is critically reviewed and findings, limitations and implications are examined. No definitive, long-term studies have been published comparing the holistic (intellectual, emotional and physical) health of appropriately matched and aged, fully vaccinated and completely unvaccinated children. As well, methodological limitations of existing studies have been identified. Four small but comprehensive studies provide data, which shows that there are evidentiary questions regarding long-term vaccine safety. Potentially significant personal and economic consequences of vaccination, as well as vaccination compliance issues, are identified. It is recommended that national health authorities and independent researchers should address these issues to facilitate a truly scientific comparison of immunisation options by parents as well as governments.