Bacterial flagellin, a potent intestinal innate immune activator, prevents murine rotavirus (RV) infection independent of adaptive immunity. The flagellin-induced immunity is mediated by Toll-like receptor (TLR5) and Nod-like receptor C4 (NLRC4), which elicit the production of interleukins 22 (IL-22) and IL-18, respectively. Here, we assessed whether a high abundance of flagellin at the time of vaccination would negatively affect the RV vaccine take. Fecal samples were collected from infants at 7 days post first dose of Rotarix vaccination to establish (a) vaccine shedders (n = 50) and (non-shedders (n = 44). QPCR was used to assay the abundance of flagellin and expression of flagellin-encoding fliC, TLR5, NLRC4, IL-22 and IL-18 genes. There was no difference in abundance of flagellin between vaccine shedders and non-shedders ( p = 0.15). However, the expression of FliC was increased 7.5-fold in non-shedders versus shedders ( p = 0.001). Similarly, TLR5 ( p = 0.045), and not NLRC4 ( p = 0.507,) was significantly expressed in non-shedders versus shedders. The expression of IL-22 ( p = 0.054), and not IL-18 dependent NLRC4 ( p = 0.650), was increased 3.4-fold in non-shedders versus shedders. Collectively, our observations suggest that the abundance of viable flagellated bacteria at the time vaccination can negatively impact the performance of RV vaccines.