Chlorotoxin (CTX) is a small peptide with unique targeting properties towards gliomas and other tumors of the neuroectodermal origin. Despite being investigated in many in vivo and in vitro targeted drug delivery and imaging studies, the mechanism of interaction between CTX and tumor cells has not been well understood. This study presents a new approach in monitoring the biochemical and biophysical changes in glioma cells after being exposed to CTX using Attenuated Total Reflection Fourier Transform Infra-Red (ATR-FTIR) spectroscopy. In the first part, we characterized the signature spectra of CTX and U87 cells. Next, we evaluated the differences in biochemical compositions of the spectra of the glioma cells treated with and without CTX over different incubation time periods. Our results indicated biochemical changes in U87 cells at different stages of incubation with CTX, with the most notable changes occurring after 30min of incubation. Detailed comparisons of the spectra of the U87 cells treated with and without CTX for 30min revealed distinct changes and shifts of the bands associated with proteins and lipids. In particular, a downshift of the band assigned to CH2 scissoring of lipid membranes from 1454cm−1 to 1448cm−1 followed by an appearance of a new shoulder at wavenumber of 1465cm−1 revealed conformational changes in hydrocarbon chain packing in lipid bilayers of U87 cells due to CTX. Other band shifts indicated additional changes in conformation and orientation of lipids and proteins in U87 cells exposed to CTX.