Giardia duodenalis is considered the most common intestinal parasite in humans worldwide. Children are especially affected, with more severe consequences than adults. The present study was designed to determine the distribution of assemblages A and B Giardia infection in children and adults, with the use of light microscopy and polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) as diagnostic procedures, and to investigate its associations with clinical and epidemiological data collected from children and adult groups. This cross-sectional study was conducted from October 2012 to October 2013 by collecting fecal samples from 200 children and 200 adults complaining of diarrhea. Samples were subjected to parasitological examination by direct wet smear and formol-ether methods. Genotyping of G. doudenalis samples was conducted by PCR-RFLP analysis. Giardia duodenalis infection caused by assemblages A and B was identified in 60 samples, 34 from children and 26 from adults. Assemblage B was detected in 38 patients (63.34%), and assemblage A was detected in 22 patients (36.66%). Assemblage A was significantly more frequent in children with age range 2–8 yr, and assemblage B was higher in children with age range 6–16 yr old. Diarrhea frequency/day and recurrences per month affected patients infected with assemblage A (P value < 0.001) more frequently. Children infected with assemblage A presented significantly more severe diarrhea and dehydration than those infected with assemblage B (P value < 0.001). Although both Giardia assemblages A and B were identified in children and adults, assemblage A infected younger children more frequently and was more closely related to severe clinical manifestations than assemblage B.