Nanotechnology-introduced materials have promising applications as nanocarriers for drugs, peptides, proteins and nucleic acids. Several studies showed that the geometry (shape and size) and chemical properties of nanoparticles affect the kinetics and pathways of cellular uptake and their intracellular trafficking and signaling. Accurate physico-chemical characterization of nanoparticles customarily precedes their use in cell biology and in vivo experiments. However, a fact that is easily overlooked is that nanomaterials decorated with organic matter or resuspended in aqueous buffers can be theoretically contaminated by fungal and bacterial microorganisms. While investigating the effects of extensively characterized PEGylated carbon nanotubes (PNTs) on T lymphocyte activation, we demonstrated bacterial contamination of PNTs, which correlated with low reproducibility and artifacts in cell signaling assays. Contamination and artifacts were easily eliminated by preparing the materials in sterile conditions. We propose that simple sterile preparation procedures should be adopted and sterility evaluation of nanoparticles should be customarily performed, prior to assessing nanoparticle intracellular internalization, trafficking and their effects on cells and entire organisms.