We have used transmission electron microscopy to observe the structural changes that have occurred in multi-walled carbon nanotubes (MWCNTs) because of acid treatment. After a thiolation reaction of the acid-treated MWCNTs using P4S10 in refluxing toluene, we have also used electron energy loss spectroscopy to characterize the changes on the nanotubes from sidewall functionalization. We have determined that the sulfur content bonded to the nanotubes is 0.6% in terms of the atomic content of the samples. Raman spectroscopy was used to examine the vibrational changes that occurred to the nanotubes as well as identifying new vibrational modes around 500 cm−1 characteristic of carbon-sulfur bonds.