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Background This study examines the association between active transport and perceived general health, perceived psychological wellbeing and a healthy body weight in the Netherlands. Methods Data were collected by an online questionnaire (N = 3663) in the Netherlands. Data collection was conducted over a period of one calendar year starting July 2012. Logistic regression analyses were used to investigate the association between choice of transport mode (bicycling vs car use and walking vs car use) and perceived general health, perceived psychological wellbeing and having a healthy weight respectively. The presented OR's may be interpreted as the likelihood of an average person in our dataset to have a better perceived health or body weight when choosing active transport (either bicycling or walking) over using the car for trips up to 7.5 km. Results Cycling was found to be significantly associated with a better perceived general health (OR = 1.35, 95%CI:1.07–1.70) and having a healthy body weight (OR = 1.52, 95%CI:1.28–1.79), but not with a better perceived psychological wellbeing (OR = 1.12, 95%CI:0.93–1.34). Walking was found to be significantly associated with having a healthy body weight (OR = 1.35, 95%CI:1.09–1.69), but not with a better perceived general (OR = 1.12, 95%CI:0.84–1.51) or psychological wellbeing (OR = 0.85, 95%CI:0.67–1.08). Conclusion Our results suggest that active transport use has been associated with a better perceived general health and a healthy body weight. However, more research is needed to be able to elucidate which factors cause this better health. No associations were observed between transport choice and perceived psychological wellbeing., Highlights • Active transport users experience a better perceived general health. • Active transport users are more likely to have a healthy body weight. • No association between transport choice and perceived psychological wellbeing in The Netherlands