Diseases are of particular importance for aquaculture worldwide, particularly in intensive culture. In Mexico, intensive culture of channel catfish is mainly done in floating cages. The aim of the present study was to determine the presence of the myxozoan Henneguya and the effect of site, period and host length on its prevalence in cage-cultured channel catfish. Over a year, fish were examined on six different sites. Results showed the presence of Henneguya exilis in all the farms. However, no significant effects were observed for site and season on prevalence, nor was there a correlation between host length and infection prevalence.