Cocoa is an abundant source of polyphenols, mainly flavan-3-ol monomers and polymers. In the literature, there are contradictory data on the absorption limit of procyanidins in humans. In our study, the Caco-2 cell model of intestinal epithelium was used to determine the absorption and secretion of cocoa flavan-3-ols. Three compounds: (+)-catechin, (−)-epicatechin and procyanidin B2 were detected and quantified at the receiver side of Caco-2 monolayer after 2 h transport experiment. The obtained results of apparent permeability coefficient suggest paracellular route of transport of investigated compounds. Additionally, the results suggest that compounds of cocoa powder purified extract are able to affect tight junction functioning.