Monocytes are important for innate immunity and include the classical (CD14brightCD16negative), intermediate (CD14brightCD16dim) and non-classical (CD14dimCD16bright) monocyte subsets. The quantification of these functionally different subsets in peripheral blood may become useful for diagnosis and follow-up in human diseases. The aim of the present study was to investigate how different pre-analytical parameters influence analysis of monocyte subsets in peripheral blood samples. We determined relative levels of monocytes and monocyte subsets by flow cytometry of peripheral blood samples derived from healthy individuals. A gating strategy exclusively extracting viable CD14+ monocytes and focusing on the three monocyte subsets was applied. We investigated the effects of (i) various anticoagulants (i.e. Li-Heparin, ACD-A, K2EDTA), (ii) insufficient filling of blood sampling tubes, (iii) cryopreservation. In addition, we analysed expression of the CCR2 chemokine receptor. The relative numbers of CD14+ monocytes depended on the anticoagulant used, whereas the fraction of the three monocyte subsets did not. Insufficient filling of blood sampling tubes altered the relative levels of monocytes out of leukocytes, but not the relative levels of the monocyte subsets. Finally, the fraction of CD14+ monocytes out of isolated peripheral blood mononuclear cells was not significantly altered by cryopreservation, but the relative percentages of monocyte subsets was altered (similar effects for ACD-A and K2EDTA samples) and this was observed in correlation to a decreased CD16 expression. Analysis of the monocyte subsets (i.e. classical, intermediate, non-classical) in peripheral blood samples requires a careful standardization of peripheral blood sampling and pre-analytic handling of the samples with respect to the anticoagulant used, filling of sample tubes, and cryopreservation of cells prior to analysis.