The aim of this study was to analyse the behaviour of the stress score (SS) and the Neperian logarithm of 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.