We aimed to demonstrate the existence of cancer stem cells in human pancreatic cancer, and to clarify that they are alpha-fetoprotein (AFP) producing cells. Six cell lines derived from human pancreatic cancers were examined, and AsPC-1 and PANC-1 were noted to express AFP. Single cell culture assays and xenotransplantation revealed that the AFP-producing cells had the capacity for self-renewal and differentiation, and that these cells were tumorigenic. Furthermore, they were resistant to anti-cancer agents. The ABCA12 transporter was expressed in the AFP-producing cells at a level more than twice as high as that in the non-AFP-producing cells. The AFP-producing cells were shown to be putative pancreatic cancer stem cells. Furthermore, the expression of ABCA12 appears to be associated with drug resistance.