Gemcitabine, 2-deoxy-2,2-difluorocytidine (dFdC), is a drug approved for use against various solid tumors. Clinically, this moderately toxic nucleoside analog causes peripheral neuropathy, hematological dysfunction, and pulmonary toxicity in cancer patients. Although these side effects closely mimic symptoms of mitochondrial dysfunction, there is no direct evidence to show gemcitabine interferes with mitochondrial DNA replication catalyzed by human DNA polymerase ␥. Here we employed presteady state kinetic methods to directly investigate the incorporation of the 5-triphosphorylated form of gemcitabine (dFdCTP), the excision of the incorporated monophosphorylated form (dFdCMP), and the bypass of template base dFdC catalyzed by human DNA polymerase ␥. Opposite template base dG, dFdCTP was incorporated with a 432-fold lower efficiency than dCTP. Although dFdC is not a chain terminator, the incorporated dFdCMP decreased the incorporation efficiency of the next 2 correct nucleotides by 214-and 7-fold, respectively. Moreover, the primer 3-dFdCMP was excised with a 50-fold slower rate than the matched 3-dCMP. When dFdC was encountered as a template base, DNA polymerase ␥ paused at the lesion and one downstream position but eventually elongated the primer to full-length product. These pauses were because of a 1,000-fold decrease in nucleotide incorporation efficiency. Interestingly, the polymerase fidelity at these pause sites decreased by 2 orders of magnitude. Thus, our pre-steady state kinetic studies provide direct evidence demonstrating the inhibitory effect of gemcitabine on the activity of human mitochondrial DNA polymerase.Many nucleoside analogs are potent anti-cancer and antiviral drug compounds. Among 15 Food and Drug Administration-approved nucleoside analogs, gemcitabine or 2Ј-deoxy-2Ј,2Ј-difluorocytidine (dFdC, 4 supplemental Fig. 1) is an anticancer drug that is clinically used for the treatment of nonsmall cell lung cancer (1), pancreatic cancer (2), metastatic breast cancer (3), and ovarian cancer (4). It has also shown promising efficacy for the treatment of other solid tumors and hematological malignancies (5-12) suggesting more widespread use in the future. In addition to its use as a monotherapy, gemcitabine is often most effective when used as part of a combination therapy, frequently with platinum-based and topoisomerase-targeted chemotherapeutic agents (13-15).Gemcitabine is administered in the form of a biologically inactive prodrug that first permeates the cellular membrane by facilitated diffusion (16, 17) almost exclusively via the human equilibrative nucleoside transporter number 1 (17, 18). Following transport, dFdC is metabolized to the biologically active monophosphorylated form (dFdCMP) by deoxycytidine kinase, which is the rate-limiting step during the activation of gemcitabine (19). Subsequently, dFdCMP is further phosphorylated to form the cytotoxic metabolites gemcitabine diphosphate (dFdCDP) and gemcitabine triphosphate (dFdCTP) by cellular kinases. It has been shown that dFdCTP com...