Abstract Biobanking is an operational component of various epidemiological studies and clinical trials. Although peripheral blood is routinely acquired and stored in biobanks, the effects of specimen processing on cell composition and clinically relevant functional markers of T cells still require a systematic evaluation. In this study, we assessed 25 relevant T cell markers in human PBMCs and showed that the detection of nine membrane markers (e.g., PD-1, CTLA4, KLRG1, CD25, CD122, CD127, CCR7, and others reflecting exhaustion, senescence, and other functions) was reduced among at least one T cell subset following standard processing, although the frequency of CD4, CD8, and regulatory T cells was unaffected. Nevertheless, a 6-mo-long cryopreservation did not impair the percentages of cells expressing many other membrane and all the eight tested intracellular lineage or functional T cell markers. Our findings uncover that several clinically relevant markers are particularly affected by processing and the interpretation of those results in clinical trials and translational research should be done with caution.