Aim The motives for smoking among the academic community and especially their variations across faculties are not known. The staff of the University of Tartu, Estonia, was therefore surveyed for smoking habits. Subjects and methods In 1992 and 2003, 519 smokers were asked why they wanted to continue smoking. The prevalence of each motive was calculated, also adjusting for sex, age, survey time, marital status, occupational class and faculty. Results 41 % of the subjects smoked for enjoyment, followed by habit (30 %), calming (29 %), company (25 %) or addiction (23 %), and 16 % smoked because it was an aid when engaged in mental work. During 1992 to 2003, the prevalence of various motives increased by 4-29 percentage units among men and 11-44 percentage units among women. Men in the faculty of mathematics and computing often smoked for enjoyment (69 %), and they often smoked as an aid when engaged in mental work (38 %) as did men in the faculty of philosophy (27 %)-prevalences 18-29 percentage units higher than those in the medical faculty. Common motives among women were: habit (70 %) and company (64 %) in the faculty of economy, addiction in that of law (63 %), enjoyment in the library (48 %) and calming in the faculty of philosophy (45 %)-prevalences exceeding those in the medical faculty by 16-60 percentage units. Conclusion The motives for smoking vary depending on the faculty, in different ways in men and women. We assume that distinct professional cultures and Estonia's transition during the 1990s underlie the findings. The results are useful in targeting anti-smoking interventions.