In the analysis of circulating tumor cells or in the preimplantation genetic diagnosis it is frequently necessary to examine one single cell. Some methods are appropriate to isolate single cells: Laser Assisted Microdissection, magnetic cell separation or FACS. The use of the whole genome amplification methods are needful, because the amount of the DNA extracted from the isolated cells is very low and inappropriate for additional examinations. With different molecular biological methods (e.g. sequencing, chip-technology) it is possible to determine genetic alterations in the analysed cells, and to return the modified cells with in vitro gene technological methods (viral vectors, non viral methods). Our aim is to summarize the methods and the possible technical problems developing during the process of the single cell molecular biological analysis.