Poly(acrylic acid) (PAA)-patterned polystyrene (PS) substrates were prepared by ion beam lithography to control cell behaviors of mouse fibroblasts and human embryonic kidney cells. Thin PAA films spin-coated on non-biological PS substrates were selectively irradiated with energetic proton ions through a pattern mask. The irradiated substrates were developed with deionized water to generate negative-type PAA patterns. The surface characteristics of the resulting PAA-patterned PS surface, such as surface morphology, chemical structure and composition and wettability, were investigated. Well-defined 100 mu m PAA patterns were effectively formed on relatively hydrophobic PS substrates by ion beam lithography at higher fluences than 5 x 10(14) ions/cm(2). Moreover, based on the in vitro cell culture test, cells were adhered and proliferated favorably onto hydrophilic PAA regions separated by hydrophobic PS regions on the PAA-patterned PS substrates, and thereby leading to the formation of well-defined cell patterns.