Nanobiointerfaces were prepared based on an electrically conductive polyethylenedioxythiophene (PEDOT). Thin (<100 nm), ultrasmooth (roughness (R-rms) < 5 nm), and functionalized PEDOT films have been successfully electropolymerized using aqueous microemulsion. The microemulsion polymerization is found to be catalyzed in the presence of a low concentration of acid and allows for film formation from various functionalized ethylenedioxythiophenes (EDOTs) (e.g., EDOT-OH, C-2-EDOT-COOH, C-4-EDOT-COOH, C-2-EDOT-NHS, EDOT-N-3) and their mixtures. The nanobiointerfaces are compositionally tunable and controlled to deposit on selected electrode surfaces. They prefer orthogonal growth on patterned surfaces and are synthesized within seconds. These thin PEDOT films exhibit very low intrinsic cytotoxicity and display no inflammatory response upon implantation, making them ideal for biosensing and bioengineering applications.