In a case-control study including 11,033 participants (The Multiple Environmental and Genetic Assessment of risk factors for venous thrombosis study) on risk factors of venous thrombosis, we studied the effect of flight-related behaviour on the risk of venous thrombosis after air travel. Patients and control subjects received a questionnaire on risk factors for venous thrombosis, including recent travel history and details of their last flight. From this population, 80 patients and 108 control subjects were selected who had recently (<8 weeks) travelled for more than 4 h by aeroplane. Window seating compared to aisle seating increased the risk twofold [odds ratio (OR) 2.2; 95% confidence interval (CI): 1.1-4.4], particularly in those who were obese (OR 6.1; 95% CI: 0.5-76.2). Anxiety (OR 2.5; 95% CI: 0.9-7.0) and sleeping (OR 1.5; 95% CI: 0.7-3.1) may increase the risk slightly. The risk was not affected by alcohol consumption (OR 1.1; 95% CI: 0.5-2.4). Flying business class may lower the risk (OR 0.7; 95% CI: 0.2-1.8). We did not find a protective effect for several measures currently part of standard advice from airlines and clinicians, i.e. drinking non-alcoholic beverages, exercising or wearing stockings. The effect of behavioural factors during flying on the risk of venous thrombosis after air travel is limited. Current advice on prevention of travel-related thrombosis may have to be reconsidered.