Cell therapy based on the use of human stem cells is more complicated than transfusion or organ transplantation because cells may undergo many additional manipulations due to different treatments for isolation, expansion, differentiation, and other types of biological changes. These manipulations require the approval of regulatory agencies (other than ethical) and the processes must be monitored with more tests than the ones applied for minimally manipulated cells. The clinical safety and efficacy of transplanted cells depend on several factors such as homologous or non-homologous sources, extent of manipulation, and culture conditions. Moreover, the kind of information needed to address these issues may differ depending on whether the cells are to be used for tissue reconstruction or repair, or to recover metabolic functions. Also anatomical site, functional integration as well as duration of therapy, are crucial points that indirectly can influence safety. Many important assays have been suggested for environmental monitoring as well as to standardize microbiological controls in stem cell banks to prevent contamination. In order to guarantee safety two main aspects must be considered: one is related to the source of cells (the donor) and the other is depending on cell collection and processing. In this review we critically analyze the steps of the processes (from collection to banking) and consider the main factors involved in the clinical research (continuously in evolution) by suggesting a standardized facsimile form to use in the laboratory for the assessment of the microbiological risk related to the cell manipulations.