Introduction: Active transportation has been associated with excess body weight in some populations but the evidence relies mostly on the use of the body mass index (BMI, weight/height), a useful but crude indicator. We analysed associations of walking and cycling assessed separately with more specific obesity markers such as waist circumference, a marker of abdominal obesity related to cardio-metabolic risk. Method: A new tool (Sedentary, Transport and Activity questionnaire) was designed, validated vs. accelerometry and doubly labelled water (Mensah BMC Public Health 2016) and then self-administered to 55,694 participants (70% women) of an on-going web-cohort (NutriNetSanté)(Menai IJBNPA 2015). In 12,776 subjects, obesity measures were taken during a clinical visit including percent body fat (bio-impedance) and waist circumference. Associations between walking, cycling and obesity markers were analysed by multivariate regression models accounting for age, gender, socioeconomic status, urban density and diet. Results: Walking > 2.5 h/week was associated in women only with lower percent body fat (-1.1%) and waist circumference (-1.7 cm) in addition to lower weight (-1.8 kg)(all p < 0.001). Cycling > 1.5 h/week was associated in both men and women with lower percent body fat (-2.5 and -1.9% respectively) and waist circumference (-4.4 and -2.1 cm) in addition to lower weight (-4.3 and -1.4 kg) (all p < 0.001). Results were unaltered with further adjustment on household and leisure physical activity. Conclusion: Walking and cycling were favourably associated with abdominal fatness. Active transportation needs to be part of public health policies focused on prevention of obesity and promotion of metabolic health.