Dielectrophoresis (DEP) represents an electrokinetic approach for discriminating and separating suspended cells based on their intrinsic dielectric characteristics without the need for labeling procedure. A good practice, beyond the physical and engineering components, is the selection of a buffer that does not hinder cellular and biochemical parameters as well as cell recovery. In the present work the impact of four buffers on biochemical, morphological, and mechanical parameters was evaluated in two different cancer cell lines (Caco-2 and K562). Specifically, MTT ([3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide]) assay along with flow cytometry analysis were used to evaluate the occurring changes in terms of cell viability, morphology, and granulocyte stress formation, all factors directly influencing DEP sorting capability. Quantitative real-time PCR (qRT-PCR) was instead employed to evaluate the gene expression levels of interleukin-6 (IL-6) and inducible nitric oxide synthase (iNOS), two well-known markers of inflammation and oxidative stress, respectively. An additional marker representing an index of cellular metabolic status, i.e. the expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, was also evaluated. Among the four buffers considered, two resulted satisfactory in terms of cell viability and growth recovery (24 h), with no significant changes in cell morphology for up to 1 h in suspension. Of note, gene expression analysis showed that in both cell lines the apparently non-cytotoxic buffers significantly modulated IL-6, iNOS, and GAPDH markers, underlining the importance to deeply investigate the molecular and biochemical changes occurring during the analysis, even at apparently non-toxic conditions. The selection of a useful buffer for the separation and analysis of cells without labeling procedures, preserving cell status, represents a key factor for DEP analysis, giving the opportunity to further use cells for additional analysis.