Mycobacterium paratuberculosis is the known cause of Johne's disease in cattle and has been implicated as a cause of Crohn's disease in humans. Concern has been expressed that the organism, which is excreted in milk and faeces of infected cattle, may be transmitted via pasteurised milk. This is largely from work that has shown an unacceptable risk of survival of the organism when it is present in raw milk at numbers exceeding 102 cfu/ml. Three possible reasons for this apparent heat resistance were investigated viz. use of a milk heating menstruum, presence of a heat resistant sub–population, and the tendency of the organism to form clumps. Heat resistance studies using a combined acid–fast/viability stain, and a comparison of the relative heat sensitivities of clumped and de-clumped M. paratuberculosis cells provided circumstantial evidence that it is the organism's tendency to form clumps which confers the apparent heat resistance. This work casts doubt on the efficacy of current commercial pasteurisation heat treatments (72°C/15s) for the inactivation of M. paratuberculosis. This would be of concern if a link between M. paratuberculosis and Crohn's disease is eventually established.