Co-crystals are crystalline complexes of two or more molecules bound together in crystal lattices through noncovalent interactions. The solubility and dissolution properties of co-crystals can allow to increase the bioavailability of poorly water-soluble active pharmaceutical ingredients (APIs). It is currently believed that the co-crystallization strategy should not induce changes on the pharmacological profile of the APIs, even if it is not yet clear whether a co-crystal would be defined as a physical mixture or as a new chemical entity. In order to clarify these aspects, we chose indomethacin as guest poorly aqueous soluble molecule and compared its properties with those of its co-crystals obtained with 2-hydroxy-4-methylpyridine (co-crystal 1), 2-methoxy-5-nitroaniline (co-crystal 2), and saccharine (co-crystal 3). In particular, we performed a systematic comparison among indomethacin, its co-crystals, and their parent physical mixtures by evaluating via HPLC analysis the API dissolution profile, its ability to permeate across intestinal cell monolayers (NCM460), and its oral bioavailability in rat. The indomethacin dissolution profile was not altered by the presence of co-crystallizing agents as physical mixtures, whereas significant changes were observed by the dissolution of the co-crystals. Furthermore, there was a qualitative concordance between the API dissolution patterns and the relative oral bioavailabilities in rats. Co-crystal 1 induced a drastic decrease of the transepithelial electrical resistance (TEER) value of NCM460 cell monolayers, whereas its parent mixture did not evidence any effect. The saccharin-indomethacin mixture induced a drastic decrease of the TEER value of monolayers, whereas its parent co-crystal 3 did not induce any effects on their integrity, being anyway able to increase the permeation of indomethacin. Taken together, these results demonstrate for the first time different effects induced by co-crystals and their parent physical mixtures on a biologic system, findings that could raise serious concerns about the use of co-crystal strategy to improve API bioavailability without performing appropriate investigations.