ZnT2 (zinc transporter-2) expression is restricted to tissues with unique zinc requirements such as mammary and prostate glands. We previously determined that ZnT2 plays a major role in zinc export from mammary glands, as women with a mutation in the gene encoding ZnT2 (SLC30A2) had an approximately 75% reduction in milk zinc concentration. Two distinct human ZnT2 isoforms (approximately 42 and 35 kDa) are predicted to result from alternative splicing of SLC30A2. We examined the localization and function of each ZnT2 isoform, in cells generated to express ZnT2-HA (haemagglutinin) fusion proteins. The 42 kDa isoform was localized primarily to the endosomal/secretory compartment and overexpression resulted in increased zinc vesicularization. In contrast, the 35 kDa isoform is associated with the plasma membrane. Importantly, zinc transport was higher in cells over-expressing each isoform, indicating that both proteins are functional. Endogenous expression of the secretory vesicle-associated ZnT2 isoform predominates in mammary cells and expression is higher in secreting cells, whereas the smaller isoform plays a minor role in zinc export, directly reflecting the secretory function of the mammary gland. Together our data shed further light on the complex integration of cellular zinc transport mechanisms, which may be facilitated by multiple isoforms of specific zinc transporters with unique cellular functions.