<b><i>Background:</i></b> Few studies have examined which lifestyle factors relate to the development of fat distribution. Therefore, the identification of the determinants of changes in fat deposition is highly relevant. <b><i>Methods:</i></b> The association between the change in physical activity (PA) and the subsequent changes in regional body fat distributions was examined. In total, 1,236 men and 1,201 women were included at baseline and participated in the Danish MONICA (MONItoring Trends and Determinants in CArdiovascular Disease) study. A questionnaire was used to assess PA at 5 and 11 years after baseline examination, while waist circumference (WC) and hip circumference (HC) were measured at both follow-ups. <b><i>Results:</i></b> Among men, WC increased in the constant active group to a lesser extent than in the non-constant active group (3.4 vs. 4.1 cm; p = 0.03) concerning leisure time physical activities (LTPA). A similar pattern was observed for both WC and HC in relation to occupational physical activities (OPA) (p = 0.02). Among women, the results went in the same direction for LTPA, whereas the associations with OPA were in the opposite direction (p = 0.001). <b><i>Conclusion:</i></b> LTPA and OPA were associated with reduced subsequent 6-year changes in regional fat distribution for men. For women, no associations were observed in relation to WC; however, OPA seemed to increase HC among women.