Although the live attenuated yellow fever (YF) 17D vaccine is considered to be one of the safest vaccines in the world today, several cases of disease associated with administration of the vaccine have been reported, including YF vaccine-associated viscerotropic disease (YF-VAVD), which was first described in 1996. All YF-VAVD isolates sequenced to date have shown very little genomic change when compared to their parental vaccine strains. In this study, we report the characterization of an isolate, BeH291597 (Brazil75), from a 1975 fatal case of YF-VAVD in Brazil. Comparison of Brazil75 with the genomic sequence of the parental 17DD vaccine strain revealed two amino acid substitutions (at positions M-49 and NS4B-240) that were unique to Brazil75. Although still a rare occurrence, this isolate suggests that YF-VAVD has been present much longer than previously recognized.