There is an ongoing effort to obtain molecular level information from living cells using surface-enhanced Raman scattering (SERS) not only to understand changes of cellular processes upon exposure to external stimuli but also to decide the status of cells; whether they are healthy or abnormal. In our research effort, we investigate how much information can be obtained from living cells to use for decision making about the cellular processes using SERS. The undertaken studies include cytotoxicity assessment of the nanomaterials and differentiation of the healthy and cancer cells. In the first case, A549 (lung cancer) and HDF (human dermal fibroblast) cells were incubated with 50 nm gold nanoparticles (AuNP) and exposed to three different nanoparticles (Zinc oxide nanoparticles (ZnO NPs), titanium dioxide nanoparticles (TiO2) and single walled carbon nanotubes (SWCNTs)) to perform SERS analysis and track the cellular response to these nanomaterials (NMs). After the principal component analysis on the spectral data, it was shown that the NPs exposed samples could be differentiated through SERS. In the second case, SERS spectra obtained from human kidney adenocarcinoma (ACHN), human kidney carcinoma (A-498) and non-cancerous human kidney embryonic cells (HEK 293) were used to diagnose metastatic, primary and non-cancerous cell lines. Linear discriminant analysis (LDA) based on principal component analysis (PCA) was applied to collected multidimensional SERS spectral data set to differentiate three different cell lines.