Side population (SP) cells, characterized by a specific Hoechst dye efflux pattern by flow cytometry were isolated from kidney hematopoietic tissues of ginbuna carp (Carassius auratus langsdorfii). The hematopoietic activity of SP cells was evaluated by the repopulation and multilineage potential using an in vivo transplant system of ginbuna carp (donor) and ginbuna-goldfish hybrids (recipient). In a flow cytometric (FCM) analysis, a small and distinct population of ginbuna SP cells displayed efficient effluxes of Hoechst 33342 was virtually identical to the efflux observed in mammalian SP cells. The frequency of the ginbuna SP cells was 0.17+/-0.08% in the kidney hematopoietic cells. Morphologically, SP cells were composed of small lymphocyte-like cells having a thin-layered cytoplasm and a round nucleus. These characteristics of ginbuna SP cells were very similar to those of mammalian SP cells. Since cyprinid fish have two hematopoietic sites, the head (anterior) and body (posterior, trunk) kidney, the distribution of SP cells were examined in head and body kidney. The proportion of SP cells were 0.33+/-0.15% in the body kidney, but near 0% in the head kidney. After the ginbuna SP cells were injected into ginbuna-goldfish hybrids, the major types of donor-derived cells (erythrocytes, neutrophils, basophils, monocytes, thrombocytes, T and B lymphocytes) were detected in the recipient blood over a long period (9-16 months post-transplantation). In ginbuna carp, SP cells reside in the body kidney and contain primitive populations of hematopoietic stem cells (HSCs).