Aims: We discuss several factors that are critical for heat inactivation experiments and which should be taken into account for future research. Methods and Results: On the basis of examples from the literature we discuss critical factors influencing the calculated heat inactivation of Mycobacterium avium subsp. paratuberculosis (MAP). Furthermore, using a modelling approach, we show that tailing of the inactivation curve of MAP is caused by the presence of cell clumps and not by a more heat-resistant cell fraction. Conclusions: The experimental conditions of the MAP heat inactivation studies of different research groups vary significantly and lead to considerable differences in results and conclusions. Therefore, a more consensual approach should be employed in future studies. In addition, our model on clumping of MAP can be used to predict the decimal reduction of MAP during heat treatment and to study the effect of clumping on other lethal effects. Significance and Impact of the Study: We discuss several factors that should be carefully considered in heat resistance experiments. This is essential for a thorough interpretation of results from experiments and should be given proper attention in future experiments and publications on this topic.