Plant polyphenols quercetin and naringenin are considered healthy dietary compounds; however, little is known of their effect on the probiotic Lactobacillus rhamnosus GG (LGG). In this study it was discovered that both quercetin and naringenin produced temporary inhibition of LGG growth, particularly at 8 hours post inoculation, with LGG eventually recovering from this suppression. The observed growth inhibition was regarded as a phenotypic response of LGG to the polyphenols; we hypothesized that the subsequent recovery was due to unknown, underlying genetic factors. The molecular response of LGG to quercetin and naringenin was determined through RNA analysis using the Helicos single molecule sequencing platform. The expression profiles of LGG grown in the presence of either quercetin or naringenin were divergent from each other, with only a few similarities, indicating that these polyphenols inhibit growth through separate mechanisms. LGG treated with quercetin demonstrated upregulation of genes associated with DNA repair and transcriptional regulation, and a decrease in expression of genes involved in metabolism and protein movement through the cell wall. LGG treated with naringenin resulted in an increase of genes associated with metabolism, and a decrease in genes involved in stress response. Results from this study demonstrate that there is a clear interaction between the polyphenols quercetin and naringenin and the probiotic LGG. The RNA expression analysis provides unique insight into the molecular response of LGG to quercetin and naringenin, revealing an identifiable pattern of gene expression.