The aim of this study was to assess the impact of the choice of threshold on physical activity patterns measured in adolescents under free living conditions (FLC) using a uniaxial accelerometer. The study comprised 2043 adolescents (12.5-17.5 years) participating in the HELENA Study. Participants wore a uniaxial accelerometer for 7 days. The PA patterns were assessed using thresholds determined from six different studies. For each of the thresholds used, the number of adolescents fulfilling the recommendation of 60 min of moderate to vigorous PA (MVPA) per day was also calculated. A significant difference was found between thresholds regardless of the activity level: differences of 38%, 207%, 136%, and 2780% for sedentary, light, moderate, and vigorous intensity PA, respectively (P < 0.001). Time of MVPA varied between methods from 25.3 to 55.2 min center dot day(-1). The number of adolescents fulfilling the recommendation varied from 5.9% to 37% according to the thresholds used. The kappa coefficient for concordance in the assessment of the number of adolescents achieving the PA recommendations was generally low. The definition of the threshold for PA intensity may considerably affect the PA patterns in FLC when assessed using a uniaxial accelerometer and the number of participants fulfilling the recommendations.