We describe the in situ synthesis of nanometer thick films of polystyrene (PS) on a self-assembled monolayer (SAM) on gold by surface-initiated free radical polymerization and further demonstrate that three-dimensional polymer structures with micrometer lateral resolution and nanometer vertical resolution can be fabricated by combining microcontact printing (mu CP) with surface-initiated polymerization (SIP). We implemented SIP onto a COOH-terminated SAM on gold using a sequential approach to couple an amine-terminated free radical initiator to the terminal COOH groups presented by the SAM, followed by free radical polymerization of styrene. Each step of SIP was characterized by X-ray photoelectron spectroscopy and ellipsometry, and the PS film and micropattern were also characterized by atomic force microscopy. We typically obtained PS films with a thickness of 10-20 nm for a polymerization time of 12-24 h and with a root-mean-square roughness of less than or equal to 50.5 nm. PS micropatterns were also successfully fabricated by reactive mu CP of the initiator onto a COOH-terminated SAM, followed by SIP of styrene. We also demonstrate two potential applications of SIP in biomaterials research: (1) label-free, real-time monitoring of protein adsorption on polymers by surface plasmon resonance (SPR) on nanometer thick homogeneous polymer films fabricated on a SAM on gold and (2) patterning cells on micropatterned polymers fabricated by combining mu CP and SIP.