Pythiosis, a life-threatening infectious disease of humans and animals in tropical and subtropical countries, is caused by the fungus-like organism Pythium insidiosum. As diagnosis of pythiosis is difficult, delayed diagnosis of pythiosis leads to poor prognosis. We developed an immunoperoxidase staining assay using rabbit anti-P. insidiosum antibodies to detect P. insidiosum directly in infected tissues of 19 patients with vascular (n = 11), ocular (n = 7) or cutaneous (n = 1) pythiosis. Tissue sections from 31 patients with various fungal infections were included as controls. Tissue sections from all pythiosis patients and 2 patients with Fusarium infections were stained positive, whereas the other 29 control sections were stained negative. Sensitivity and specificity of the assay was 100% and 94%, respectively. Based on the prevalence of human pythiosis (2%), calculated positive predictive value and negative predictive value was 24% and 100%, respectively. Thus, the diagnostic value of this assay is for ruling out pythiosis. The assay requires routine laboratory equipments and can easily be performed by pathologists in rural hospitals where the disease is more prevalent.