Carbon nanotubes (CNTs) have been promoted as nanodevices in the biomedicine areas of diagnosis and therapy. In terms of drug delivery, CNTs could be useful in the case of hydrophobic drugs and multiple codeliveries of therapeutic and imaging molecules. Epithelial cells, being specialized in absorption and secretion, are the first barrier to overcome. At the same time, several frequent tumors are of epithelial origin (cervix, ovarian, liver). Synchrotron-based imaging and spectroscopic techniques are suitable tools to follow the fate of nanodrugs in epithelial cells. We present an example of multi-microscopy approach combining soft X-ray spectromicroscopy at the TwinMic beamline (Elettra Synchrotron, Trieste, Italy) with light and Scanning Electron (SEM) microscopies. In particular, we show that 2–4 h exposure to SWCNTs is not toxic (no viability changes) to a model of cervical epithelial cells, even though it causes temporary perturbation in the membrane and intracellular structures of exposed cells.