Health status indicators in Uganda have recently shown much awaited improvement after a long lull of stagnation and reversal. The EPI programme has been credited with some of the success in the reduction of Infant and Child Mortality. It has ensured and sustained high immunisation coverage through most of the country. However, as a vertical programme, it has used some approaches which come into question by the article. This article gives a critical analysis of the challenges facing Uganda in the struggle to sustain the currently high immunisation coverage rates. The three challenges singled out for future attention by the programme are establishing mechanisms to monitor imported cases of controlled diseases from unstable regions of neighbouring countries, maintaining the crucial and more effective routine immunisation in the face of the more lucrative mass immunisation campaigns and sustaining constant availability of immunisation resources.