We performed researches in early postoperative period after transplantation of tissue-engineered trachea, seeded with autologous mononuclear cells. We studied the different biological active molecules in peripheral blood from patients after transplantation of tissue-engineered trachea using ELISA test. The measuring of the concentration of ICAM, VCAM, E-selectin, VEGF and EPO showed the increasing level with significantly maximum concentration on 6 – 12 posttransplantation days. Interestingly that the levels of inflammatory cytokines such as TNF-a, IL- and IL-2 were decreased those days. Flow cytometry was used to study of population of cells from peripheral blood. The first day after transplantation the hematopoietic cells CD34+ were found. We observed the cells with phenotype CD34-CD45-CD105+CD73+CD144+ appeared between 6 – 14 days after transplantation. Our results indicate the activation of progenitor and mesenchymal stem cells. Thus, we examined the dynamics of biologically active molecules and stem cells in the peripheral blood of patients after transplantation of tissue-engineered trachea with seeded autologous mononuclear cells.