Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB) (APR0228/2008), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq/MCT) and Universidade Federal da Bahia (UFBA), Brazil.Techniques for Giardia diagnosis based on microscopy are usually applied as routine laboratory testing; however, they typically exhibit low sensitivity. This study aimed to evaluate Giardia duodenalis and other intestinal parasitic infections in different pediatric groups, with an emphasis on the comparison of Giardia diagnostic techniques. Feces from 824 children from different groups (diarrheic, malnourished, with cancer and from day care) were examined by microscopy and ELISA for Giardia, Cryptosporidium sp. and Entamoeba histolytica coproantigen detection. Giardia-positive samples from day-care children, identified by either microscopy or ELISA, were further tested by PCR targeting of the β-giardin and Gdh genes. Statistically significant differences (P<0.05) were observed when comparing the frequency of each protozoan among the groups. Giardia duodenalis was more frequent in day-care children and Cryptosporidium sp. in diarrheic and malnourished groups; infections by Entamoeba histolytica were found only in children with diarrhea. Considering positivity for Giardia by at least one method, ELISA was found to be more sensitive than microscopy (97% versus 55%). To examine discrepancies among the diagnostic methods, 71 Giardia-positive stool samples from day-care children were tested by PCR; of these, DNA was amplified from 51 samples (77.4%). Concordance of positivity between microscopy and ELISA was found for 48 samples, with 43 confirmed by PCR. Parasite DNA was amplified from eleven of the 20 Giardia samples (55%) identified only by ELISA. This study shows the higher sensitivity of ELISA over microscopy for Giardia diagnosis when a single sample is analyzed and emphasizes the need for methods based on coproantigen detection to identify this parasite in diarrheic fecal samples.