Aims/hypothesis: The aim of the study was to analyse how strongly commuting and leisure-time physical activity affect progression to diabetes and to study whether this relationship is different in individuals with isolated impaired fasting glucose (i-IFG) and isolated impaired glucose tolerance (i-IGT). Methods: We studied the incidence of diabetes in 4,031 individuals without diabetes at baseline who participated in the baseline and 5 year follow-up examinations of a population-based primary prevention study, the Inter99 Study. Glucose tolerance status at baseline and at follow-up were based on OGTTs. Commuting and leisure-time physical activity at baseline were assessed by questionnaire. We present rate ratios from Poisson regression analyses adjusted for relevant confounders. Results: The progression rate to diabetes was lower among physically active individuals in the total study population and particularly among those with i-IGT. The associations were attenuated and lost statistical significance after further adjustment for BMI. We observed no impact of physical activity on the progression to diabetes in individuals with i-IFG. Conclusions/interpretation: Physical activity was associated with a lower progression to diabetes in the total study population and in individuals with i-IGT, a condition primarily characterised by muscle insulin resistance. Physical activity did not predict progression to diabetes in individuals with i-IFG, a condition primarily characterised by hepatic insulin resistance. Our results suggest that there is a differential relationship between physical activity and progression to diabetes among those with i-IFG and i-IGT. Therefore, clinical trials testing the effect of physical activity on progression from i-IFG to diabetes are needed. Trial registration:: ClinicalTrials.gov ID No.: NCT00289237 Funding:: The Danish Medical Research Council, the Danish Center for Evaluation and Health Technology Assessment, Novo Nordisk, Copenhagen County, the Danish Heart Foundation, the Danish Diabetes Association, the Danish Pharmaceutical Association, the Augustinus Foundation, the Ib Henriksen Foundation and the Becket Foundation.