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Abstract Background The scientific literature questions the impact of stretching exercises performed immediately before muscle strengthening exercises on different components of musculoskeletal physical fitness. Pilates is a physical exercise modality that typically uses stretching exercises preceding muscle-strengthening exercises. However, no studies have investigated the effects of stretching in a Pilates program on components of musculoskeletal fitness. The aim of the present study was to verify the effects of stretching in a Pilates exercise program on flexibility, strength, vertical jump height and muscular endurance. Methods Thirty-two sedentary young women were randomized into two groups: traditional Pilates (TP), who performed flexibility and muscle strengthening exercises (n = 16), and nontraditional Pilates (NTP), who only performed muscle-strengthening exercises (n = 16). Sessions took place 3 times a week for 8 weeks. The following tests were performed pre- and postintervention: 10-RM knee extensors, vertical jump, handgrip, 1-min sit-ups, Sorensen and sit-and-reach. The occurrence of adverse events was recorded throughout the intervention and compared between groups using odds ratio (OR). To compare the results of motor tests between groups, ANCOVA or Mann‒Whitney U test was used for parametric and nonparametric data, respectively. The data were analyzed by intention-to-treat. Results After intervention, the TP was superior to NTP for the sit-and-reach test, with a large effect size (d = 0.87; p = 0.035), with no differences between groups for the other tests. Intragroup comparisons showed significant differences (p |