The present work constitutes a prospective study on a total of 97 pediatric patients; 65 cancerous patients and 32 non-cancerous patients suffering from diarrhea. All faecal specimens were examined parasitologically using the MZN and EIA techniques. Samples testing positive for Cryptosporidium were examined using the PCR-RFLP technique which amplified the Cryptosporidium oocyst wall protein (COWP) gene. Among 97 diarrheic pediatric cases, 47 (48.5%) were positive by nested PCR. Rsa I digestion of nested PCR product of COWP gene revealed the presence of 2 genotypes: genotype 1 in 32 (68%) and genotype 2 in 15 (32%) of cases. In this study, comparable correlations were observed between the clinical parameters associated with the 2 genotypes as there were no statistically significant associations between genotypes and age, sex, vomiting, abdominal pain or fever or dehydration. The fact that Genotype 1 was found to be relatively more prevalent than genotype 2 among all groups of patients examined suggests a relatively greater risk of human source of infection than zoonosis.