Chagas disease, caused by the flagellate protozoan Trypanosoma cruzi, is characterized by considerable variation in both incidence and infection severity. This variation has been attributed to a set of complex features including the host genetic background, environmental and social factors, and the genetic heterogeneity of parasite populations. Using biochemical and molecular markers these populations can be divided into two major groups (TCI and TCII). In a previous work, our group identified cysteine and metalloprotease activities as good markers for differentiating TCI from TCII wild isolates, with a higher level of heterogeneity observed among TCII isolates. In this investigation, we applied the protease activity assay to a sample of 49 sylvatic T. cruzi isolates that had been previously assessed in terms of their Swiss mice infection patterns. Protease activity profiles were determined at pH 5.5 and 10.0 and was compared with the original host species, phylogenetic lineage, and mice infection characteristics. Substantial variability, with molecular weights ranging from 35 to 220 kDa for active proteases at pH 5.5, and of 30 to 90 kDa for active proteases at pH 10.0, was observed in gelatin substrate gels, with no phenetic separation between TCI and TCII groups or original hosts. The combinatorial expression of proteases recorded among individual isolates may account for the diverse behavior observed for parasite populations in nature.