The development of molecular genetics has greatly enhanced the study of Toxoplasma gondii, and investigations into the biology and pathology associated with neosporosis will be similarly benefited by the development of molecular tools for Neospora caninum. We have demonstrated the feasibility of using the existing DNA vectors developed for T. gondii to transfect and transform the Nc-1 strain of Neospora. We have also shown that T. gondii proteins are faithfully expressed and targeted in N. caninum, indicating the suitability of using Neospora as a heterologous expression system for studying T. gondii. These studies provide the basis for initiating molecular genetic studies on N. caninum and will allow for a number of molecular comparisons of these two closely related, though phenotypically distinct, parasites. Here we describe the methods and reagents used to perform genetic manipulations of N. caninum, and we present some of the principles and potential utilities of these molecular studies, including the use of N. caninum as a heterologous system for the study of T. gondii proteins.