The authors describe a case of severe debilitating diarrhea due to isosporiasis in a two year old child, a known case of systemic vasculitis receiving prolonged corticosteroids therapy, an association rarely reported previously. It was refractory to treatment with dihydrofolate reductase inhibitor combined with sulfonamide such as cotrimoxazole to which isosporiasis usually responds well and is being described here for clinical interest and uniqueness of its presentation and laboratory findings.