Background: Younger and older generations may differ substantially in their lifetime smoking habits, which may result in generation-specific health challenges. We aimed to quantify generation shifts in smoking over a period of 25 years. Methods: We used the Doetinchem Cohort Study (baseline 1987-1991; 7768 individuals; 20-60 years; follow-up 1993-2012) and the Longitudinal Aging Study Amsterdam (baseline 1992-1993; 3017 individuals; 55-85 years; follow-up 1995-2009). Generation shifts were studied between 10-year generations (age range: 20-100 years). Generation shifts were examined graphically and by using logistic random effect models for men and women. Results: Among men, significant generation shifts in current smoking were found between two non-successive generations: for instance men in their 40s at baseline smoked much more than men in their 40s at follow-up (33.6% vs. 23.1%, p < 0.05). Among women, the most recently born generation showed a favourable significant generation shift in current smoking (-7.3%) and ever smoking (-10.1%). For all other generations, the prevalence of ever smoking among women was significantly higher in every more recently born generation, whereas no other generation shifts were observed for current smoking. The unfavourable generation shifts were mainly found among the lower educated. Conclusions: The future burden of disease due to smoking is expected to be reduced among men, but not yet among women. Educational differences in smoking-related health problems are expected to increase.