15Bacterial vaginosis is a common condition among women of reproductive age and is 16 associated with potentially serious side-effects, including an increased risk of preterm birth. 17Recent advancements in microbiome sequencing technologies have produced novel insights into 18 the complicated mechanisms underlying bacterial vaginosis and have given rise to new methods 19 of diagnosis. Here we report on the validation of a quantitative, molecular diagnostic algorithm 20 based on the relative abundances of ten potentially pathogenic bacteria and four commensal 21Lactobacillus species in research subjects (n = 172) classified as symptomatic (n = 149) or 22 asymptomatic (n = 23). We observe a clear and reinforcing pattern among patients diagnosed by 23 the algorithm that is consistent with the current understanding of biological dynamics and 24 dysregulation of the vaginal microbiome during infection. Using this enhanced assessment of 25 the underlying biology of infection, we demonstrate improved diagnostic sensitivity (93%) and 26 specificity (90%) relative to current diagnostic tools. Our algorithm also appears to provide 27 enhanced diagnostic capabilities in ambiguous classes of patients for whom diagnosis and 28 medical decision-making is complicated, including asymptomatic patients and those deemed 29 "intermediate" by Nugent scoring. Ultimately, we establish CLS2.0q as a quantitative, sensitive, 30 specific, accurate, robust, and flexible algorithm for the clinical diagnosis of bacterial vaginosis -31 importantly, one that is also ideal for the differential diagnosis of non-BV infections with 32 clinically similar presentations. 33 34