Multiwalled carbon nanotubes (MWCNTs) have attracted huge attention due to their multifunctionality. Their unique properties allows for covalent and noncovalent modifications. The most simple method for functionalization of carbon nanotubes is their decoration with the oxygen containing moieties which can be further simultaneously functionalized for design of new class carriers for targeting and imaging. Here, we present methodology for chopping nanotubes, characterization of MWCNTs, the effect of size on the biocompatibility in culture of L929 mouse fibroblasts using WST-1, LDH and apoptosis assays. The analysis provides the optimal carbon nanotubes length and concentration which can be used for functionalization in order to minimize the effect of the secondary agglomeration when interacting with cells.