Abstract Antimicrobial peptides are key effector molecules throughout nature responsible in part for the defense against microbial pathogens and influencing the composition of colonizing microbes. Defensins are the major antimicrobial peptides produced by Paneth cells in the mammalian small intestine and are essential for maintaining homeostasis between host and gut microbes. While other defensins have potent microbicidal activity, human Paneth cell alpha defensin 6 (HD6) lacks such activity, yet provides protection from invasion by enteric bacterial pathogens. Using a transgenic mouse model expressing HD6 in Paneth cells, we reported the importance of HD6 in preventing the translocation of pathogenic Salmonella Typhimurium (STM) across the small intestinal epithelium (doi:10.1126/science.1218831); however, the mechanism underlying the inhibition of invasion is not fully understood. We hypothesize that HD6 binds to extracellular bacterial protein structures, such as flagella, and inhibits swimming motility through a process of direct binding and self-assembly. Using a semi-solid agar based motility assay, we demonstrate Salmonella radially migrate from the site of inoculation at a slower rate when in the presence of HD6. In ongoing studies using live epifluorescence microscopy to observe GFP-expressing STM in the presence of HD6, we observe a dramatic decrease in STM motility in a concentration dependent manner with some STM appearing to be completely immobilized, but without changes in bacterial viability. With these findings in mind, we plan to expand our investigation to include both structural variants of HD6 and mutants of STM to more clearly define the key elements of peptide and bacteria that mediate this activity.