Drug modification with nanomaterials is a new trend in pharmaceutical studies and shows promising results, especially considering carbon-based solutions. Graphene and its derivatives have attracted much research interest for their potential applications in biomedical areas as drug modifiers. The following work is a comprehensive study regarding the toxicity of ciprofloxacin (CIP) modified by graphene oxide (GO). The influence on the morphology, viability, cell death pathway and proliferation of T24 and 786-0 cells was studied. The results show that ciprofloxacin modified with graphene oxide (CGO) shows the highest increase in cytotoxic potential, especially in the case of T24 cells. We discovered a clear connection between CIP modification with GO and the increase in its apoptotic potential. Our results show that drug modification with carbon-based nanomaterials might be a promising strategy to improve the qualities of existing drugs. Nevertheless, it is important to remember that cytotoxicity effects are highly dependent on dose and nanomaterial size. It is necessary to conduct further research to determine the optimal dose of GO for drug modification.