In this study, we utilized a model of trout intestinal explants to investigate the uptake and the metabolic effects of Hydroxytyrosol (HT), a bioactive molecule belonging to polyphenols, present in the fruit and leaf of the olive (Olea europaea L.). Fragments of the pyloric caeca (PC), mid intestine (MI) and distal intestine (DI) of the rainbow trout Oncorhynchus mykiss, were incubated with varying concentrations (2.0–20–200 μM) of HT for 5, 15, 60, 120 and 360 min. HT was uptaken by PC and MI, but not DI. The HT concentration reached the highest value after 15 min of incubation. 2.0 and 20 μM HT were well tolerated by both PC and MI, 200 μM HT was cytotoxic, causing DNA damage in PC, but not in MI. 1H NMR analysis of PC and MI incubated with 2.0 and 20 μM HT revealed the increase in the essential amino acids and fatty acids, suggesting that HT slowed down the amino acid degradation while acting as lipolysis stimulators. The effect of HT on the intestinal macromolecular asset was also investigated by Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR) in order to test the advantages of this method in the analysis of biological samples. HT caused macromolecular modifications coherent with the results of the HT uptake, cytotoxicity and 1H NMR analysis.In conclusions, the intestinal explants allow many experimental conditions to be tested simultaneously. Such ex vivo approach may be usefully employed to study the effects of additives or feed components in screening tests before designing in vivo trials. Thus, it may represent an alternative to reduce the number of animals employed. Finally, the present study confirms the validity of ATR-FTIR as a rapid, non-invasive, high-resolution analytical method of analysis for biological samples.