This review summarizes recent advances in understanding the role of the nitric oxide (NO) and cyclic GMP (cGMP) pathway in stem cells. The levels of expression of various components of the pathway are changed during the differentiation of pluripotent embryonic stem cells. In undifferentiated stem cells, NO regulates self-renewal and survival predominantly through cGMP-independent mechanisms. Natriuretic peptides influence the growth of undifferentiated stem cells by activating particulate isoforms of guanylyl cyclases in a cGMP-mediated manner. The differentiation, recruitment, survival, migration, and homing of partially differentiated precursor cells of various types are sensitive to regulation by endogenous levels of NO and natriuretic peptides produced by stem cells, within surrounding tissues, and by the application of various pharmacological agents known to influence the cGMP pathway. Numerous drugs and formulations target various components of the cGMP pathway to influence the therapeutic efficacy of stem cell-based therapies. Thus, pharmacological manipulation of the cGMP pathway in stem cells can be potentially used to develop novel strategies in regenerative medicine.