Milk protein hydrolysates generated with different starting substrates, including sodium caseinate (NaCN), acid casein (Acid CN), skim milk powder (SMP) and glycomacropeptide (GMP) were demonstrated to behave as serotonin 2C (5-HT(2C)) receptor agonists. The 5-HT(2C) receptor activating potential of NaCN hydrolysates correlated with an increased protein hydrolysis, most likely due to enhanced release of bioactive peptides over the time course of hydrolysis. In its unhydrolysed form, GMP was the only starting substrate showing 5-HT(2C) serotonin receptor agonist activity. The 5-HT(2C) serotonin receptor agonist activity of its corresponding hydrolysate (GMPH-240 min) was significantly higher (P < 0.05). Fractionation of the 240 min NaCNH using ultrafiltration (UF), solid-phase extraction (SPE), semi-preparative reverse-phase high performance liquid chromatography (RP-HPLC) and isoelectric focusing (IEF) was carried out. Characterisation of the fractions obtained shows that the bioactive peptides had a relatively low molecular mass (<1 kDa), were hydrophobic in nature and had a pI between 8.6 and 13.2. These different physicochemical characteristics together with the stability of NaCNH-240 min to simulated intestinal digestion, allow prediction of a favourable outcome regarding the bioavailability of the bioactive peptides therein. These results reinforce the potential of milk-derived bioactive peptides to be developed into functional foods targeted at 5-HT(2C) receptor modulation.