With the advances in the studies of body composition, it has been observed that several factors can interfere with the estimates of relative body fat using the skinfold thicknesses method. Therefore, the purpose of this study was to investigate the impact of the use of different skinfold calipers for the analysis of body composition by skinfold thicknesses measurements. Two hundred and fifty nine male subjects (23.3 ± 2.9 years) took part of the study. Nine skinfold thicknesses were measured (abdominal, subscapular, suprailiac, triceps, biceps, midaxillary, chest, medial calf, and thigh) using the Lange (USA) and the Cescorf (Brazil) calipers with accuracy of 1.0 and 0.1 mm, respectively. Significant differences were found in the comparison between the two calipers on all the investigated skinfold thicknesses (1.8 to 31.0%) with highest values obtained by the Lange caliper (p < 0.01). When these values were applied to four different predictive equations, developed by different researchers, the body fat estimate was significantly modified (p < 0.01), resulting in differences of 5.2 to 6.9%. Results indicate that the use of different skinfold calipers may maximize the errors of estimation produced by different predictive equations used for the analysis of body composition.