Hematopoietic stem cells (HSCs) are capable of self-renewal and differentiation into all blood cell types. During adult life, they reside in the bone marrow in a quiescent state. By contrast, in the growing embryo hematopoiesis is sequentially found in several developmental niches. This review provides an overview of the still controversial contribution of each of these embryonic sites to the final pool of adult HSCs and discusses new insights into the cellular origin and the molecular regulation implicated in the generation of blood progenitor cells. A better understanding of HSC development during ontogeny is essential to develop new strategies to amplify HSCs or to generate them from embryonic stem cells or by somatic cell reprogramming.