An efficient microfluidic system for diagnosing disease marker molecules is reported. This system is constructed with the anodic aluminum oxide (AAO) as a porous substrate, which provides havens for target proteins and their antibodies from shear force of flow. AAO is embedded on microfluidic channels, where hepatitis B virus (HBV) antibody is immobilized in the surface-modified AAO pores. The performance using porous AAO in a PDMS microfluidic device is comparable to that of conventional ELISA system for the detection of hepatitis B surface antigen (HBsAg).