| Summary: | <i>Giardia duodenalis</i> is a significant contributor to the burden of diarrheal disease in sub-Saharan Africa. This study assesses the occurrence and molecular diversity of <i>G. duodenalis</i> and other intestinal parasites in apparently healthy children (<i>n</i> = 311) in Ibadan, Nigeria. Microscopy was used as a screening method and PCR and Sanger sequencing as confirmatory and genotyping methods, respectively. Haplotype analyses were performed to examine associations between genetic variants and epidemiological variables. At microscopy examination, <i>G. duodenalis</i> was the most prevalent parasite found (29.3%, 91/311; 95% CI: 24.3–34.7), followed by <i>Entamoeba</i> spp. (18.7%, 58/311; 14.5–23.4), <i>Ascaris lumbricoides</i> (1.3%, 4/311; 0.4–3.3), and <i>Taenia</i> sp. (0.3%, 1/311; 0.01–1.8). qPCR confirmed the presence of <i>G. duodenalis</i> in 76.9% (70/91) of the microscopy-positive samples. Of them, 65.9% (60/91) were successfully genotyped. Assemblage B (68.3%, 41/60) was more prevalent than assemblage A (28.3%, 17/60). Mixed A + B infections were identified in two samples (3.3%, 2/60). These facts, together with the absence of animal-adapted assemblages, suggest that human transmission of giardiasis was primarily anthroponotic. Efforts to control <i>G. duodenalis</i> (and other fecal-orally transmitted pathogens) should focus on providing safe drinking water and improving sanitation and personal hygiene practices.
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