The present work constitutes a prospective study on children suffering from diarrhoea; including 60 paediatric cancer patients and 60 paediatric non-cancerous patients as a control group. All faecal specimens were examined parasitologically using the AFT, MTS and MZN staining techniques. Among 60 diarrhoeic paediatric cancer cases, 16 (26.7%) were positive for microsporidia by using both AFT and MTS staining techniques. On the other hand, Cryptosporidium were detected in 6 (10.0%) of cases using both AFT and MZN staining techniques. The agreement between the AFT technique with the MTS and MZN staining technique was statistically highly significant by Kappa statistics (K = 0.66, P < 0.001). In this study, comparable correlations were observed between the clinical parameter associated with the 2 parasites with statistically significant associations between microsporidiosis and female sex; cryptosporidiosis and abdominal colics. The presence of loose stool was statistically significant with microsporidiosis. Co-infection with microsporidia and yeast cells was proved statistically significant with P-value <0.05.The findings indicate that Microsporidia and Cryptosporidium are important agents in the cause of diarrhoea among paediatric cancer patients and direct microscopical examination is needed in such immunosuppressed patients to avoid possible complications by such opportunistic parasites.