Five Trypanosoma cruzi stocks were isolated from infected patients in the central state of Jalisco, Mexico. Parasites were isolated by direct inoculation of infected blood into BALB/c mice. The five stocks of T. cruzi were analyzed for in vitro growth, and for virulence and parasitic load in vivo. Furthermore, a genetic analysis based on restriction fragment length polymorphism associated with a repetitive element from the rRNA gene spacer was performed. No differences in in vitro growth or in parasitic load in vivo were found among the stocks. While three stocks showed low virulence for mice, the other two stocks killed 80 and 100% of the infected mice. In addition, Southern blot of total DNA hybridized with a repetitive element from the rRNA gene spacer showed two clearly distinct patterns that correlated with the observed ability of the stocks to kill infected mice. Our results show a correlation among the ability to kill BALB/c mice, the genetic pattern and clinical symptoms produced by the different stocks in the infected patients.