trans-Sialidase (TS) is an enzymatic activity described only for trypanosomes that is involved in the invasion of host cells by Trypanosoma cruzi. The enzyme that is shed by the parasite is made of two domains, the C-terminal region containing immunodominant amino acid repeats that define the SAPA antigen and the N-terminal domain that contains the putative region for enzymatic activity. The SAPA antigen induces a strong humoral response detected shortly after infection, both in humans and in mice. This response is directed to the immunodominant domain but is irrelevant in terms of neutralization of TS activity. We now show that TS activity can be detected in sera from acutely infected mice. However, mice infected with a T. cruzi strain whose growth can be controlled by the host did not have detectable levels of TS activity in sera. In fact, sera from these mice were able to abolish TS activity. This inhibition was due to the presence of specific antibodies directed against the enzymatic domain of the protein since they also abolish the activity of a recombinant molecule lacking the immunodominant amino acid repeats. The neutralizing antibodies were present from day 30 after the infection, while antibodies to the immunodominant repeats were detected by day 8 postinoculation, suggesting that the in vivo role of these repeats is to defect the humoral response to the repeat domain until the infection is established.