is the most common non-viral sexually transmitted infection. 5-nitroimidazoles are the only FDA-approved medications for treatment. However, 5-nitroimidazole resistance has been increasingly recognized and may occur in up to 10% of infections. We aimed to delineate mechanisms of resistance using transcriptome profiling of metronidazole (MTZ)-resistant and sensitive clinical isolates. In vitro, 5-nitroimidazole susceptibility testing was performed to determine minimum lethal concentrations (MLCs) for isolates obtained from women who had failed treatment ( = 4) or were successfully cured ( = 4). RNA sequencing, bioinformatics, and biostatistical analyses were performed to identify differentially expressed genes (DEGs) in the MTZ-resistant vs. sensitive isolates. RNA sequencing identified 304 DEGs, 134 upregulated genes and 170 downregulated genes in the resistant isolates. Future studies with more isolates with a broad range of MLCs are needed to determine which genes may represent the best alternative targets in drug-resistant strains.