BACKGROUND: In studies of recurrent events, it is common to consider a person who has suffered a disease episode and received curative treatment to be not at risk of suffering a new episode for a duration of time. It is a common practice to deduct this duration from the person's observation time in the statistical analysis of the incidence data. METHODS: We examined the concepts of incidence and protective efficacy from a real life point of view. We developed simple formulae to show the relationship between the incidence rate and protective efficacy between analyses with and without deducting the curative treatment time from the observation time. We used a malaria chemoprevention and a malaria vaccine study, both previously published, to illustrate the differences. RESULTS: Applying the formulae we derived to a range of disease incidence that covered the two case studies, we demonstrated the divergence of the two sets of estimates when incidence rate is approximately 1 per person-year or higher. In the malaria chemoprevention study, incidence was 5.40 per person-year after the deduction of curative treatment time from observation time but 4.48 per person-year without the deduction. The chemoprevention offered 56.6 and 50.7% protection calculated with and without the deduction, respectively. In the malaria vaccine study, where disease incidence was much lower than one, the results between the two ways of analysis were similar. For answering real life questions about disease burden in the population in a calendar year and the reduction that may be achieved if an intervention is implemented, the definition without deduction of curative treatment time should be used. CONCLUSIONS: The practice of deducting curative treatment time from observation time is not wrong, but it is not always the best approach. Investigators should consider the appropriateness of the two analytic procedures in relation to the specific research aims and the intended use of the results.