Intestinal cells are continuously exposed to food whose components are able to modulate some of their physiological functions. Among the bioactive food derivatives are casein phosphopeptides (CPPs), coming from the in vitro or in vivo casein digestion, which display the ability to form aggregates with calcium ions and to increase the uptake of the minerals in differentiated intestinal human HT-29 and Caco2 cells. Since extracellular calcium is a known inactivator of the TRPV6 channel, which is also involved in the colon cancer progression, the present study aims to determine a possible modulation by CPPs of the molecular structures responsible for paracellular and/or transcellular calcium absorption in these two cell lines. The paracellular calcium transport was determined by TEER measurements in Caco2 cells and by Lucifer Yellow flow in HT-29 cells. The possible modulation of transcellular calcium absorption machinery by CPPs was investigated by determining the mRNA expression for both the TRPV6 calcium channel and the VDR receptor in 1,25(OH)₂D₃ pre-treated undifferentiated/differentiated cells. The results obtained point out that: (i) CPPs do not affect paracellular calcium absorption; (ii) 1,25(OH)₂D₃ increases the TRPV6 mRNA expression in both types of cells. In the case of HT-29 cells this is the first determination of the presence of the TRPV6 channel; (iii) CPPs per se are not able to affect the VDR and TRPV6 mRNA expression; (iv) CPP administration does not affect the TRPV6 mRNA expression in 1,25(OH)₂D₃ pre-treated HT-29 cells and Caco2 cells. Unlike peptides coming from the digestion of cheese whey protein digest, the digestion of milk casein produces peptides with no effects on TRPV6 calcium channel expression, though the same peptides are able to determine a calcium uptake by the intestinal cells.