Functionalized carbon nanotubes are increasingly exploited as innovative components for the development of advanced biomedical devices. In this study we report a novel synthetic route for the formation of single-walled carbon nanotube (SWCNT)–polyaniline (PANI) hybrids by in situ chemical polymerization. The surfactant sodium dodecylsulfate (SDS) is used as a template for monomer assembly and polymerization. The resulting composite preserves the surfactant and is characterized by a tight binding between SWCNTs and PANI. Having the idea of integrating these new types of SWCNT conjugates into advanced biomedical tools (i.e. implantable multi-electrode arrays), we explored their potential impact on the viability and function of cells from the immune system. We have compared the cytotoxic effects of SWCNT-COOH, SWCNT/SDS and SWCNT/SDS/PANI on mouse spleen cells and macrophages. The results indicate that biocompatibility of the different SWCNT conjugates is dependent both on the doses used and the type of cells.