The restorative capacity of human CD34(+) hematopoietic cells is clinically used in the autologous and allogeneic transplant setting to support cytotoxic therapy. We examined gene expression patterns of highly enriched bone marrow CD34(+) (BM-CD34(+)) or G-CSF-mobilized peripheral blood CD34(+) (PB-CD34(+)) cells by cDNA array technology, quantitative real-time RT-PCR, and flow cytometry, to identify molecular causes underlying the functional differences between circulating and sedentary hematopoietic stem and progenitor cells. The greater cell cycle and DNA synthesis activity of BM-CD34(+) compared to PB-CD34(+) cells was reflected by the 2- to 5-fold higher expression of 9 genes involved in cell cycle, 11 genes regulating DNA synthesis, and the cell cycle-initiating transcription factor E2F-1. The 2- to 3-fold greater expression of 5 pro-apoptotic genes in PB-CD34(+) cells indicated a higher apoptotic activity, which could functionally be corroborated by apoptosis assays. Thrombin receptor (PAR1), known to play a role in trafficking of malignant cells, was 3.6-fold higher expressed in circulating CD34(+) cells than in BM-CD34(+) cells. Guidance via thrombin receptor might molecularly mediate stem cell migration. In summary, our study provides gene expression profiles of primary human CD34(+) hematopoietic cells of blood and marrow. Our data molecularly confirm and explain the finding that CD34(+) cells residing in the bone marrow are cycling more rapidly, whereas circulating CD34(+) cells consist of a higher number of quiescent stem and progenitor cells. Moreover, our data give novel molecular insights into stem cell migration and differentiation.