The smooth surface structure of intracortical microelectrodes implanted within the nanometer‐scale architecture of brain tissue may contribute to the foreign body response. Here, the neuroinflammatory response to nanopatterning surface grooves etched directly on nonfunctional Michigan‐style microelectrodes is explored. Rats implanted with nanopatterned silicon microelectrodes are compared to smooth control implants to observe the effects the grooves have on neuroinflammation. Histology and real‐time PCR at 2 and 4 weeks postimplantation quantify glial cell reactivity and activation, inflammation, oxidative stress, and neuronal survival. Histological observations of glial cells and blood–brain barrier permeability do not show appreciable differences between the nanopatterned and control implants. However, silicon microelectrodes with nanopatterned grooves have more high mobility group box 1 (HMGB1) gene expression at 2 weeks and less nitric oxide synthase (NOS2) gene expression at 4 weeks compared to control surfaces. Control samples have increased NOS2, HMGB1, and tumor necrosis factor gene expression from 2 to 4 weeks, while nanopatterned implants have significant decrease in CD14 gene expression from 2 to 4 weeks. Collectively the results indicate that etching nanopatterned grooves do not reduce histological markers of neuroinflammation compared to control implants, but gene expression results encourage further investigation.