The calcofluor stain (CF), the monoclonal antibody (MAb) 3B6 indirect immunofluorescence assay (IFA) and the modified trichrome blue stain (MT) were compared in terms of their reproducibility in a routine laboratory and in order to evaluate the percentage of cases of microsporidiosis in Portuguese HIV patients. A total of 166 faeces samples, 71 pulmonary specimens and 43 urine samples were studied using the 3 techniques. CF had a high sensitivity and a moderate specificity when applied to faeces samples. The sensitivity was lower with pulmonary specimens. The method is easy and quick to perform but readings take a long time to obtain. The MAb 3B6 IFA had a good to excellent sensitivity when applied to faeces and urine samples, but moderate sensitivity in pulmonary specimens. Readings were quick and easy to obtain, but the assay took longer to perform than the other 2 techniques. There was a greater correlation between the results obtained with the MT and MAb 3B6 IFA techniques than between those obtained with the MT and CF techniques. In conclusion, the MT performed better than the MAb 3B6 IFA and CF and continues to have an important place in a routine laboratory for the diagnosis of microsporidiosis. This work also confirms the existence of a relatively high proportion (30%) of cases of infection with Microsporidia, especially intestinal microsporidiosis, in HIV patients in Portugal.