Zika virus (ZIKV) is a mosquito-transmitted positive-sense RNA virus in the family Flaviviridae. Candidate live-attenuated vaccine (LAV) viruses with engineered deletions in the 3 prime UTR provide immunity and protection in animal models of ZIKV infection, and phenotypic studies show that LAVs retain protective abilities following in vitro passage. The present study investigates the genetic diversity of wild-type (WT) parent ZIKV and its candidate LAVs using next generation sequencing analysis of five sequential in vitro passages. ZIKV RNA from was transfected into Vero cells, incubated for nine days, harvested, and clarified by centrifugation to generate passage 0 (P0) ZIKV infectious clones. Subsequently, P0 ZIKVs were blind-passaged into fresh cultures to generate P1, then serially through P5. P1-P5 stocks were harvested from cell media at 4-5 days post-infection. ZIKV RNA from 3 prime UTR deletion mutants were transfected into Vero cells, incubated for nine days, harvested, and clarified by centrifugation to generate passage 0 (P0) ZIKV infectious clones. Subsequently, P0 ZIKVs were blind-passaged into fresh cultures to generate P1, then serially through P5. P1-P5 stocks were harvested from cell media at 4-5 days post-infection. Genetic diversity of the viruses were assessed by evaluating both the variability (or uncertainty) at each nucleotide position was determined using Shannon entropy calculations and identified single nucleotide variants (SNVs).