Enteroparasites in children from three marginal urban districts of Trujillo (Peru) were studied to treat these children and to design a prevention and control programme. A total of 845 children were examined. The general prevalence of enteroparasites was of 66.3%, and 45.6% were multiparasitized. The pathogenic enteroparasite prevalence were 23.8% (Giardia lamblia), 4.6% (Iodamoeba buschlii), 2.6% (Cyclospora cayetanensis), 2.2% (Hymenolepis nana), and 2% (Cryptosporidium spp.). G. lamblia was the most frequent parasite both in diarrheic children (28.1%) as well as in nondiarrheic ones (19.5%). The G. lamblia genotypes were molecularly characterized by sequence analysis of the glutamate dehydrogenase (gdh) gene using PCR and RFLP. Sequence analysis revealed both Assemblage A (AI and AII) and Assemblage B (BIV), with the predominance of Assemblage AI. All the samples with Assemblage A were diarrheic but not those with Assemblage B. This is the first study of molecular characterization of G. lamblia in Peruvian children and confirms the importance of asymptomatic patients in the transmission of the giardiosis, especially in places with poor hygiene and sanitation.