Cadmium (Cd), tungsten (W), tellurium (Te), beryllium (Be), and lead (Pb), are non-essential metals pervasive in the human environment. Studies on athletes during training periods compared to non-training control subjects, indicate increased loss of minerals through sweat and urine. The aim of this study was to compare the level of these trace elements, determined by inductively coupled plasma mass spectrometry (ICP-MS) in urine samples, between athletes and age-matched sedentary subjects living in the same geographical area, although anthropometric and cardiovascular measurements showed that athletes have significantly (P ≤ 0.001) lower BMI, body fat and heart rate, whereas the muscle and bone percentage was significantly (P ≤ 0.001) higher than in sedentary subjects. The validity of the methodology was checked by the biological certified reference material. Trace element analysis concentrations, expressed in μg/mg creatinine, of five toxic elements in urine from athletes (n = 21) versus sedentary subjects, (n = 26) were as follows: Cd (0.123 ± 0.075 vs. 0.069 ± 0.041, P ≤ 0.05); W (0.082 ± 0.053 vs. < limit of detection); Te (0.244 ± 0.193 vs. 0.066 ± 0.045, P ≤ 0.001), Be (0.536 ± 0.244 vs. 0.066 ± 0.035, P ≤ 0.001); Pb (0.938 ± 0.664 vs. 2.162 ± 1.444 P ≤ 0.001). With the exception of Pb, urine toxic metal concentrations from athletes were higher than from sedentary subjects. This fact suggests that physical activity counteracts, at least in part, the cumulative effect of toxic environment by increasing the urine excretion of toxic metals in trained people.