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Stroke causes an efflux of various groups of progenitor/stem cells from bone marrow to bloodstream and a rise in neuron specific enolase (NSE) serum concentrations. The aim of this study was to identify activity of chosen stem/progenitor cells during first 7 days after stroke through correlations between these cells levels and NSE values. Additional goal was to confirm the role of NSE as a prognostic marker of ischemic stroke. Venous blood was collected repeatedly from 67 acute ischemic stroke patients and 15 control subjects, in order to assess NSE with ELISA, and CD45−CD34 + CD271+, CD45−CD34 + CXCR4+, CD45−CD34 + CXCR7+ and CD45−CD34 + CD133 + stem/progenitor cells by means of flow cytometry. Patients underwent repeated assessment with the National Ischemic Stroke Scale and modified Rankin Scale. Ischemic lesion volumes were assessed twice by MRI-DWI (day 1 and 5 ± 2). NSE correlated negatively with MFI levels of the CD45−CD34 + CXCR7+ cells, and percentage levels of the CD45−CD34 + and CD45−CD34 + CXCR4+ cells. NSE concentrations were significantly higher in patients compared to control subjects. NSE on day 2 positively correlated with lesion volume on both MRI. NSE on day 2 and 6–7 correlated positively with initial NIHSS scores, and on day 1 with mRS score on day 9.In conclusion, in this study NSE indicated some activity of the CD45−CD34 + CXCR7+, CD45−CD34 + and CD45−CD34 + CXCR4+ stem/progenitor cells in the first 7 days after ischemic stroke. Additionally, this study supports the thesis that NSE might be a valuable prognostic marker in acute ischemic stroke.Ischemic stroke causes an efflux of various stem cells from bone marrow to bloodstream.Ischemic stroke causes a rise in serum neuron specific enolase (NSE).CXCR7+ and CXCR4+ stem/progenitor cells in blood correlate with NSE after stroke.NSE correlates with lesion volume, neurological and functional status after stroke.