Tet enzymes oxidise 5-methyl-deoxycytidine (mdC) to 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC) and 5-carboxy-dC (cadC) in DNA. It was proposed that fdC and cadC deformylate and decarboxylate to dC in the course of an active demethylation process. This would re-install canonical dC bases at previously methylated sites. The question whether such direct C-C bond cleavage reactions at fdC and cadC occur in vivo remains an unsolved problem. Here we report the incorporation of synthetic isotope- and (R)-2’-fluorine-labelled dC and fdC-derivatives into the genome of cultured mammalian cells. Following the fate of these probe molecules using UHPLC-MS/MS provided quantitative data about the formed reaction products. The data show that the labelled fdC probe is efficiently converted into the corresponding labelled dC, most likely after its incorporation into the genome. This allows concluding that fdC is undergoing C-C bond cleavage in stem cells that leads to the direct re-installation of unmodified dC.