The aim of the present research was to analyse the subjective and objective psychophysiological stress response of experienced and non-experienced Pharmacy and Biotechnology students in laboratory practices. We analysed in 82 Pharmacy and Biotechnology degree students divided into two groups (non-experienced: n: 53; experienced: n: 29) the autonomic stress response by the analysis of heart rate variability (HRV) before, during and after and distress perception before and after a laboratory practice. Results showed how students in both groups presented a large anticipatory anxiety response at the beginning of the practise (low HRV values). During the entire laboratory practice, non-experienced students showed a maintained sympathetic modulation while experienced students presented a higher parasympathetic modulation (high HRV values) consistent with a habituation process. Laboratory practise performed by Pharmacy and Biotechnology students produced an anticipatory anxiety response independently of their experience, but, non-experienced students showed a lower habituation response in both subjective and objective stress records than experienced students at the end of the laboratory practice.