Several analogs of hygromycin A were tested in an Escherichia coli cell free protein synthesis inhibition assay and in a Serpulina hyodysenteriae whole cell assay. The aminocyclitol moiety is essential for antibacterial activity in both cell free and whole cell assays. However a 4'-O-allyl ether of hygromycin A aglycone showed an equivalent MIC to hygromycin A, while having a less potent IC50 in the cell free assay. Hence 6-deoxy-5-keto-D-arabino-hexofuranose can be replaced by a hydrophobic allyl group and still retain antibacterial activity. However, this replacement reduces the intrinsic protein synthesis inhibition activity. The loss of intrinsic activity with replacement by the allyl group may be compensated for by better transport into the bacterial cell. In addition to the SAR analysis, we demonstrated that the ineffectiveness of hygromycin A against Gram-negative enteric bacteria such as Escherichia coli is mainly due to the efflux mechanism (Acr A/B pump) existing widely among the enteric bacteria rather than the impermeable barrier of the outer membrane.