Objectives To assess secular changes in physical fitness (PF), moderate-to-vigorous-physical activity (MVPA) and TV-viewing in 1st-grade children from Crete, Greece. Design Cross-sectional cohorts examined in academic years 1992/93 and 2006/07. Methods Two representative samples of children, aged 5.9–7.8 years, were studied during 1992/93 (N=606) and 2006/07 (N=361). PF (sit-and-reach, standing-broad-jump, sit-ups and 20m-shuttle-run-test) was assessed by the European-PF test battery and MVPA by a physical activity (PA) questionnaire. Data on the frequency of TV-viewing was also collected. Results Between 1992/93 and 2006/07, there was a significant increase in all fitness tests in both genders (P<0.001) and in MVPA in boys (76.5min/week vs. 38.7min/week, P<0.001). Time spent watching TV on weekdays was significantly more in both genders in 2006/07, compared to 1992/93 (P<0.001). In 2006/07, active boys and active girls spent more time in MVPA than active boys and girls in 1992/93 (P<0.001). Significantly higher proportions of boys and girls engaged in vigorous activities in 2006/07, than 1992/93 (P<0.001 and P=0.027, respectively). Conclusions A significant increase in physical and cardiorespiratory fitness in both genders and MVPA in boys was observed in children from Crete between 1992/93 and 2006/07. The increase in weekday TV-viewing, despite being parallel to an increase in leisure-time MVPA, could have an unfavorable effect on health and should be tackled in future interventions in this population. Dietary, anthropometric and biochemical indices should also be investigated to assess their impact on the secular changes in physical fitness and activity observed in this sample of children.