A 41-year-old diabetic woman developed Paecilomyces javanicus endocarditis and subsequent cerebral fungal embolism and vasculitis with massive infarction and hemorrhage 6 years after a mitral valve replacement with porcine heterograft. The organism was identified by the culture from the infected brain tissue and aortic valve. Cerebral infection due to fungus Paecilomyces is rare. This report documents the cerebral manifestations of fungus Paecilomyces javanicus and describes for the first time the ultrastructure of such an organism obtained from the infected tissue. Their ultrastructural findings, similar to those described in Paecilomyces farinosus derived from culture, include a double-layered cell wall, a triple unit plasma membrane, abundant cytoplasmic lipid droplets, vacuoles, membranous profiles and septal formation. This report further demonstrates hyphae with packed 50A filaments and granulofibrillary material and features suggestive of intrahyphal hyphae, not previously described in fungus Paecilomyces.