Acanthamoeba castellanii has been known to possess pathogenic properties, such as acanthamoebic keratitis and granulomatous amoebic encephalitis. The role of proteases and proteins in the pathogenesis of these infections is still poorly understood. As Acanthamoeba sp is a ubiquitous protozoon found in the natural environment they can potentially cause human infections. This study characterized cyst and trophozoite proteins of 3 environmental A. castellanii isolates in comparison with a clinical isolate, ATCC 50492. The latter and environmental IMU1 isolate had 100% genotype identity with A. castellanii and demonstrated protein spots with higher molecular weights (> 95 kDa) at relatively higher isoelectric values (> pI 7.00) compared to the two other environmental isolates (IMU4 and IMU5) that had 99% genotype identity to A. castellanii based on 16 S rDNA sequence. Thus such trophozoite proteins may be involved with the parasite's ability to cause acanthamoebic keratitis.