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Background: The US Centres for Disease Control provides a widely used online user-friendly computational program, called SAMMEC (Smoking Attributable Mortality, Morbidity and Economic Costs) to produce estimates of tobacco-related mortality. However, the SAMMEC tool loses accuracy because it lacks flexibility in deciding which diseases enter into the calculations, has estimates of relative risk (RR) attributable to smoking based on old studies, and does not allow for the latency period that occurs between initial exposure and mortality. Methods: Smoking attributable mortality (SAM) due to active smoking in Israel was estimated with the approach used by SAMMEC taking into account past and present smoking prevalence (lag-times) as well as using new and expanded disease categories. Results: Around 50.3% of the increase from the un-lagged SAM estimate of 3859 deaths to the final SAM estimate of 8664 deaths in 2003 is attributable to the introduction of lag times. More robust estimates of risk accounted for a further 29.6% of the increase. While 21.2% is attributable to the inclusion of additional disease categories, only 1.5% was attributable to the widening of existing diseases categories. Conclusion: This difference in estimates is attributable to expansion of the list of diseases included, updating the estimates of RR for smoking-attributable death, and the use of smoking prevalence from previous years to more accurately reflect the effect of tobacco use on disease occurrence. There is a need to establish an ‘authority’ to implement a multi-faceted intervention strategy to decrease the considerable burden from smoking in Israel. [ABSTRACT FROM PUBLISHER]