Close complex monitoring during the entire training period is essential for professional athletes to assess the effect of the training programme and to determine the quality of recovery. Follow-up of biochemical and hormonal variables throughout the season can help realize the above-mentioned goals. Objectives: To determine baseline blood creatine kinase (CK) and cortisol (C) levels in professional basketball players before the beginning of regular training and to follow up the subsequent levels of blood C and CK over an entire season with analysis of dynamic changes in relation to individual coefficients of variation. Methods: Six professional basketball players were monitored from the first pre-season day to the end of a regular season. Blood samples were collected at six time points: before the pre-season, after the pre-season and four times during the in-season to determine blood C and CK concentrations. Results: Individual trends of the investigated variables were established and analysed with respect to the calculated intra- and inter-individual coefficients of variation for C and CK. Dynamic changes in C and CK levels coincided with changes in the content of the training process. Conclusion: In summary, the findings in the present study suggest that long-term intensive exercise in basketball has a significant influence on the blood cortisol profile. Muscle damage was associated with bodily collisions between the players but not with stress response in the current study.