Switchgrass can generate large amounts of renewable biomass and hence is one of the most promising bioenergy crops. Improving the quality of switchgrass lignocellulosic biomass will enable its utilization for biofuels. Arabidopsis SHINE family of transcription factor SHN2 was previously identified as a master regulator of cell wall deposition in transgenic rice. However, it is unclear if the Arabidopsis SHN genes also have a similar biological function in switchgrass. Here, we generated transgenic switchgrass overexpressing the Arabidopsis SHN3 transcription factor. Compared with the wild-type, AtSHN3-overexpressing switchgrass plants were stunted in their growth. There were no significant differences in terms of lignin and cellulose content between the SHN transgenics and wild-type switchgrass plants. However, two AtSHN3 transgenic lines SHN7-2 and SHN5-2, displayed significant changes in several matrix polysaccharide monomers. Overexpression of AtSHN3 in switchgrass did not alter the stem mechanical strength when subjected to tensile-torsion analysis. Interestingly, the AtSHN3-overexpressing transgenic lines were more susceptible to switchgrass rust ( Puccinia emaculata) than wild-type plants. Therefore, AtSHN3 may have a negative role in regulating disease resistance in switchgrass.