Chagas' disease, which is an important health problem in humans, is caused by the protozoan Trypanosoma cruzi. The cellular and molecular mechanisms, involved in the selective tropism of T. cruzi to different organs remain largely unknown. In this study we designed a PCR-based molecular diagnosis method in order to study the tropism and growth kinetics of T. cruzi in a murine model infected with parasites isolated from an endemic area of Mexico. The growth kinetics and parasite tropism of T. cruzi were also evaluated in the blood and other tissues. We observed that T. cruzi isolates from the Western Mexico showed a major tropism to mouse heart and skeletal muscles in this murine model.