To examine whether physical activity (PA) is associated with changes in waist circumference (WC), and changes in WC given changes in body mass index (BMI). Longitudinal population-based study including 2026 men and 2782 women aged 21–81 years. Subjects were examined in 1991–1993 (baseline) and 2001–2003 (follow up), where height, weight and WC were measured. Information about overall PA in leisure-time (LTPA), walking, biking and sports activity was collected with self-administrated questionnaires at baseline. Outcomes were changes in WC and changes in WC given changes in BMI between baseline and follow up. The median increase in WC was 3.0 cm in men and 3.5 cm in women during follow-up, and with a considerable inter-individual variation. LTPA, walking and biking were not significantly associated with the outcomes. Inverse associations between sports activity and the outcomes were observed in both sexes, and these were significant in some analyses. Associations were not altered by adjustment for confounders or by exclusions of subjects with diseases and/or treatment by obesity-inducing medication. This study suggests that LTPA, walking and biking have no appreciable effects on changes in WC or changes in WC given changes in BMI, whereas sports activity may have small preventive effects.