Introduction Functionally capable and mature blood cells derive from a haematopietic stem cell in the bone marrow. By activating certain genes and by interaction of blood growth factors haematopoietic stem cells (HSC) have the capability of proliferating (cell growth, division) and regenerating, differentiating into a certain blood line and maturing along a specific blood line, from an immature to a functionally active, mature cell. It is because of these capabilities that blood stem cells are today an unavoidable method of curing blood diseases. Objective The purpose of this paper is to show and explain the tasks of an infallible component in blood stem cells transplantation, which is a laboratory. Data sources and methods To treat a patient, haematopoietic stem cells are collected from the bone marrow, peripheral blood and umbilical cord blood, and they can be taken from the patient (autologuous blood stem cells) or from another person (allogeneic blood stem cells, related and non related). Stem cells for autologous transplantation are taken via blood separators in the process of leukapheresis. To renew the function of the bone marrow in long-term meaning, haematopoietic stem cells obtained in the process of leukapheresis need to be processed in a laboratory. The process of HSC treatment is divided into a routine and specialized process. It is also necessary to do a quality control check of the HSC which includes: checking the number and type of cell, immunophenotypization of HSC, assesing the viability of the cells, procedure of short term HSC culture, microbiological testing and the analysis of tumor cell contamination. After all of these procedures are successfully finished, HSC are stored in liquid nitrogen on the temperature of -196 ̊C. Results HSC transplantation has enabled for a lot of patients, depending on individual factors of their disease, complete healing or long term survival. On the other hand, besides these positive outcomes as an end result certain complications linked to either collection or transplantation of HSC can appear, such as: hypocalcemia, hypomagnesemia, hypokalemia, low thrombocyte and erythrocyte number, hypothermia, infections etc. Conclusion Collecting HSC from the peripheral blood in the process of leukapheresis, and their following laboratory treatment is a more simple and safer method than collecting bone marrow. Due to its multiple advantages autologuous HSC transplantation has been used for over 25 years as a method of treating haematological and immunological diseases.