Ischemia and reperfusion (I/R) is an unavoidable condition during free flap transplantation. Restoration of blood flow is usually associated with a profound inflammatory response. Cytokines and growth factors are the functional proteins which exert their specific influence on injury or repair during the healing period. Plasma concentrations of 18 cytokines and growth factor proteins (IL6, IL8, IP10, TNFα, MCP1, Fractalkine, GRO, bFGF, GMCSF, IFNg, MIP1a, VEGF, sCD40L, IL10, TGFα, IL1β, IL12P40, and TNFβ) have been analyzed with respect to I/R status during microsurgery tissue transplantation in both, artery and vein, from patients by multiplexed immunoassay. Both technical feasibility and biostatistics data analysis approaches were thoroughly assessed. It has been found that, from all investigated proteins, the venous plasma levels of IL6 significantly increased during the ischemia period and mostly sustained their high levels during reperfusion, while venous plasma levels of IL8 showed in general a significant increase in the ischemia period followed by a rapid decrease in the reperfusion period. In conclusion, these findings direct toward an active involvement of tissue-resting leukocytes which may become therapeutic targets for concomitant medication in flap surgery to improve wound healing.