The aim of this study was to analyse whether Physical Activity Index (PAI), Physical Fitness, Screen Time (watching TV and computer use), Socio-economic Status and Commuting to School made a significant contribution to longitudinal changes in Body Mass Index (BMI) in youth. This longitudinal study was carried out over a period of 3 years with 345 students (147 boys) who were between 11 and 16 years old at the beginning of the study. Students were invited to perform tests from FITNESSGRAM Battery for Curl-Ups, Push-Ups, Back-Saver Sit and Reach, and 20 m Shuttle-Run (CRF). Fitness tests were categorized in "Healthy Zone" (HZ) and "Under Healthy Zone" (UHZ), PAI in "less active" and "active"; Socio-economic Status, in low, middle and high education level, and Commuting in active and passive. BMI was corrected for age and gender meaning that we subtracted the age-and-sex-specific cut points for overweight. Corrected body mass index was used as dependent variable in a Linear Mixed Model. The main result was the strong positive and independent association of individuals with CRF performances UHZ with corrected body mass index. In conclusion, the results of this longitudinal study showed markedly an important relationship of lower fitness levels with the risk of being overweight/obese, in particular CRF and abdominal strength.