Background: Gastrointestinal parasitic infections are one of the global health concerns in developing countries like Bangladesh. Among them, Cryptosporidium spp. plays an essential role in causing diarrhea, malnutrition, and poor cognitive function, especially in children. The study was conducted to identify the frequency of cryptosporidium cases and other parasitic agents. Methods: A Cross-sectional observational study was conducted among 219 hospitalized children with diarrhea. The conventional microscopic technique was applied for parasitic detection. A particular staining procedure was performed to identify oocysts of Cryptosporidium spp. And PCR was conducted to determine the SSU rRNA and gp60 gene of Cryptosporidium. Results: Cyst of Giardia, ova of Ascaris lumbricoides (AL), Trichuris trichiura (TT), AL, and TT were identified in 2.3%, 1.4%, 0.5%, and 0.9% samples by wet mount preparation. The distribution of Cryptosporidium spp. was 1.4% and 4.1%, which was detected by the staining method and nested PCR. Factors independently associated with Cryptosporidium infection are unsafe water, lack of regular hand washing, and insufficiency of exclusive breastfeeding. Conclusions: This is the first report to detect the frequency of Cryptosporidium and other intestinal parasites and associated factors in Chattogram city of Bangladesh.