Coccidia had been implicated as the most important opportunistic parasites in patients with acquired immune deficiency syndrome. It is transmitted via the feco-oral route. The study aimed to compare the efficacy of microscopic tests with ELISA assay for detection of oocysts in feces. This study assisted the presence of Coccidia oocyst in fecal samples of 300 patients attending Zagazig University Hospital by using modified Ziehl-Neelsen stain (MZN) ,Auramine phenol stain (AP) and Enzyme-linked immunosorbent assay. Cryptosporidium infection rate was the highest (20.7%) among other Coccidia. Mixed infection of Cryptosporidium and Cyclospora either alone or with Cytoisospora and that of Cryptosporidium and Cyclospora with concomitant Microsporidia were recorded (9.7%, 1.7% and 5% respectively) by AP and (17.7, 6.7, 1 and 3.3 % respectively) by MZN. The specificity of modified Ziehl-Neelsen was 100% for both, while the sensitivity was 77.5%, while they were 100% and 100% respectively for AP, and 100% and 91.9% for ELISA. Conclusion, this study shows that Auramine phenol is a simple fluorescent staining, promising technique in diagnosis of intestinal Coccidia as it has high sensitivity and specificity and it is less time-consuming method.