Virus, bacteria, fungi and parasites are pathogens to which individuals are constantly exposed. Pathogen recognition by cells of the immune system is carried out by a growing list of pattern-recognition receptors (PRRs) which are evolutionally conserved and absent in mammals, named pathogen-associated molecular patterns (PAMPs). PRRs can be found in extracellular matrix, within cytoplasm and on cellular membranes. Among the membrane PRRs, Toll-like receptors (TLRs) induce the production of pro-inflammatory cytokines and the expression of co-stimulatory molecules upon stimulation on mature cells, resulting in the triggering of immune danger signals. Recent reports showing the regulation of hematopoiesis by TLRs, suggest that they are involved in the most primitive stages of hematopoietic development and contribute to emergent replenishment of innate immune cells. These data entail TLRs to hematopoiesis and also revolutionize our understanding of the mechanisms governing infection responses. In this review, we focus on the most relevant findings from the TLR discovery to the use of TLR agonists and antagonists in novel therapies for infectious, autoimmune and neoplastic diseases. Of special interest is the research progress in the TLR functional expression by primitive hematopoietic stem and progenitor cells.