Aptamers represent auspicious ligands for recognition of target molecules on the surface of a specific cell population, such as stem or cancer cells. These ligands are able to capture and enrich desired cells from a cell mixture, and can be used for identification of new biomarkers, development of cell-specific therapeutics, and stem cell therapy. In this study, we investigated the influence of dead cells on single-stranded DNA (ssDNA) binding and established a method to eliminate dead cells from a cell suspension. Flow cytometry analyses demonstrated that all dead cells were stained with fluorescein-labeled ssDNA molecules. The increasing of the proportion of dead cells led to an increased number of cells that were positive for ssDNA staining. Using dead cell removal microbeads, the proportion of dead cells was significantly reduced. The studies demonstrated that dead cells lead to unspecific uptake/binding of ssDNA molecules during cell-Systematic Evolution of Ligands by Exponential enrichment (SELEX) and can cause failure of the selection process. Thus, the elimination of dead cell population before incubation with ssDNA molecules will reduce the loss of target binding sequences and the contamination of the enriched aptamer pool with unspecific ssDNA molecules caused by unspecific binding to dead cells.