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Objective This study aimed to to perform genotyping of Toxoplasma gondii strain or variant causing atypical toxoplasmic uveitis in Indonesia patients. Methods Ocular fluid samples originated from 46 uveitis patients with non-specific ocular manifestation were analyzed forToxoplasma infection by PCR of the B1 locus. The clonal type was determined by amplification, sequencing and phylogenetic analysis of SAG2 and GRA6 loci in B1-positive samples. Clinical data was obtained from the medical records. Results Pan uveitis was the most frequen