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Background Regular sport has favourable influence on the physical and mental state. Our aim was to analyse the relationship between regular sport activities, body parameters, cortisol level, perceived stress and the frequency of psychosomatic symptoms in male and female university students. Methods Subjects were university students (N = 200). They were divided in sporting (more than 7 h week−1: 56 males (sm), 50 females (sf)) and non-sporting (less than 3 h week−1: 44 males (nsm) and 50 females (nsf)) groups. Body composition was estimated by Inbody720-analyser. Stress levels were measured by (1) free cortisol level in saliva measured by using IBL-ELISA kits and (2) questionnaires about psychosomatic symptoms and perceived stress scale. Results There were significant subgroup’ differences in body composition (fat%:sm:12.1 ± 6.0 vs. nsm:17.9 ± 6.8; sf:20.8 ± 5.5 vs. nsf:25.4 ± 5.7; muscle%:sm:50.3 ± 3.6 vs. nsm:47.6 ± 3.9; sf:43.8 ± 3.2 vs. nsf:41.7 ± 3.3), and in stress level (total scores:sm:21.0 ± 5.7 vs. nsm:23.3 ± 7.2; sf:25.5 ± 7.0 vs. nsf:28.0 ± 9.7). There were gender differences in the psychosomatic symptoms' frequency (total scores: sm: 14.6 ± 6.3 vs. sf: 20.4 ± 7.4; nsm: 14.9 ± 6.1 vs. nsf: 19.6 ± 8.2). The sporting students had larger muscle, smaller fat percentages, and lower level of stress. Basic level of salivary cortisol revealed significant relation with physical activity: sporting students had lower level of cortisol. This relation was reflected in higher percentage of students with low level of cortisol in the physically active subgroups (s/ns males: 29% vs. 15%; s/ns females: 18% vs. 5%) and in the higher percentage of female students with high level of cortisol in the non-sporting subgroup (27% vs. 11%). Conclusion Regular sport activity is positively related with lower stress levels in university students.