Two major genotypic assemblages of Giardia intestinalis infect humans; the nested real-time polymerase chain reaction (PCR) was used for targeting the triose phosphate isomerase (tpi) gene to detect and genotype G. intestinalis in human feces in Egypt. Among 97 fecal samples, 30 (31%) were diagnosed as giardiasis by saline wet mount microscopy after staining with Lugol's iodine. The tpi gene was amplified from 41 (42.3%) fecal samples, of which 11 were microscopy-negative specimens. Of the total samples, 24 (58.5%) contained assemblage A group I, and 7 (17.1%) were assemblage A group II from the group of patients complaining of intermittent diarrhea. Eight (19.5%) samples contained assemblage B from patients with persistent diarrhea. Two (5%) samples had a mixture of assemblage A group II and assemblage B. The technique was able to detect as few as 20 trophozoites per PCR on fecal DNA-isolated, microscopy-negative, and quantitative (q)PCR-positive specimens; there was a higher average cycle threshold value than microscopy-positive and qPCR-positive specimens, suggesting that they represented true, low-burden infections. In conclusion, we could genotype G. intestinalis from fresh stool samples in Egypt; in infections commonly presented with intermittent diarrhea, the most prevalent genotype was assemblage A group I. The most vulnerable age group included 10- to 20-yr-old individuals.