Although the hematopoietic stem cell is an attractive target cell for gene transfer, little is known about its biology in vivo in large animals (or man). We have studied the in vivo behavior of hematopoietic stem cells in glucose-6-phosphate dehydrogenase (G6PD) heterozygous (female Safari) cats, and demonstrated that clonal instability persists for up to 4.5 years after autologous marrow transplantation. This contrasts the 2–6 months of clonal disequilibrium reported in comparable murine studies. Our data also suggests that hematopoietic stem cells do not self-renew more frequently than once per three weeks. These data may impact strategies for optimizing gene therapy in large animals, and by extension in man.