The aim of this study was to analyse the behaviour of the stress score (SS) and the Neperian logarithmof the Root Mean Square of Successive R-R Interval differences(LnrMSSD) of heart rate variability (HRV) as indicators of internal load throughout sympathetic and parasympathetic modulation, supported by biochemical parameters of internal load. 14 handball university athletes (age 22.30 ± 1.83years) were evaluated. Six times of HRV and biochemical markers were collected. Each variable were analyzed by conventional statistics and using the Cohen´s d, and Hopkins magnitude for the sample size effect. It was analyzed the Pearson correlations between variables. The LnrMSSD, SS and cortisol presented significant changes (p< .05). Correlations were found between HRV (SS and LnrMSSD) and CK respectively. Results of this study shows that SS can be a reliable method for the evaluation of internal load during competition.