The aim of the present work was to evaluate the topography of spirochetes' cells Borrelia burgdorferi s.s. B31 in atomic force microscope [AFM]. Results: The length of spirochetes B. burgdorferi has ranged between 15.38-22.68pm. The cells of spirochetes do not constitute structures of a fixed diameter and height. Thus, in order to identify real parameters of cells, the horizontal distance and vertical distance have been used in the measurements. The average value of a spirochetes’ diameter has been estimated by taking series of measures and it is 0.40 pm. The average value of a spirochetes’ height has been estimated by taking series of measures and it is 70.14 nm. The analysis of a relation between measured parameters of spirochetes: diameter and height revealed that along with the growth of diameter of a bacteria cell, its height also grows. The average value of a fibers’ diameter has been estimated by taking series of measurements and it is 0.09 um and the average height of fibers was 7.91 nm. Conclusions: The atomic force microscope (AFM) is a modern tool with a broad spectrum of observatory and measure abilities and is a technique which has been used in biology and microbiology to investigate the topography of surface and in the evaluation properties of cells.