Background An association between lower IQ of parents, measured early in life, and smoking among their offspring has been reported. The extent to which other background factors account for this association is unknown.

Methods Data on IQ, smoking, mental health, social class, parental divorce and social problems in a cohort of men born during 1949–1951 and conscripted for military service in 1969 were linked to smoking data on 682 offspring interviewed in the Swedish Surveys of Living Conditions 1984–2009.

Results In an age-adjusted model, a one-step decrease on a stanine scale was associated with an OR of 1.19 (95% CI 1.04 to 1.35) for offspring smoking. Adjusting for father's socioeconomic background and smoking, mental illness and social problems in youth only marginally lowered the OR's.

Conclusions Lower IQ among fathers measured at ages 18–20 years was associated with smoking in their offspring. The association was not explained by father's social class in childhood or a higher prevalence of mental illness, social problems or smoking measured among the fathers in their late adolescence.