Background: Coccidiosis of domestic fowl, caused by species of the Genus EIMERIA, is responsible for important economic losses in poultry production. Because different species and/or strains can vary in pathogenicity and other biological parameters, their precise characterization is important for epizootiological studies.Methods: Fifty samples from litter, whole intestinal tract and feces were collected from poultry houses located in different provinces of Iran. One hundred twenty male day-old broiler chicks were challenged with three selected isolates. Data on weight gain, Food Conversion Ratio (FCR), food intake, lesion scoring and shedding of oocysts per gram of feces were recorded and analyzed by the Duncan’s test.Results: In all treatments, the challenged groups had statistically significant lower weight gain than that of unchallenged control group. Isolate three caused the lowest weight gain and food intake and the worst lesion score as well as FCR. Despite originating from close geographical regions for isolates 1 and 2, the difference in bio pathologic factors may be either due to different proportion of identified species or the different pathogenicity of the species present in the isolates.Conclusion: The results highlight the importance of considering various species of EIMERIA in designing the preventive, control and treatment strategies to prevent coccidiosis in different regions of Iran. Further characterization of each isolate would be the next step to provide a basis for coccidiosis research with well-characterized local isolates.