Functional gastrointestinal disorders (FGIDs) are common disorders in the population. Lifestyle habits have been suspected to influence the presence and degree of symptoms, and many studies have examined the role of food components and physical activity on the disease development. The role of smoking and alcohol intake on FGID has been less thoroughly examined. This systematic literature review, of a large amount of studies from different countries around the world with different design and application of FGID criteria, shows that smoking seems to be associated with a significant 50% increased risk of FD for current compared with never smokers. The associations between smoking and other FGIDs are weak, if present at all. A moderate alcohol intake is not associated with FGIDs. On the other hand, a high alcohol intake may lead to development and aggravation of FGID symptoms, especially functional dyspepsia.