Systematic evolution of ligands by exponential enrichment (SELEX) is a screening technique that involves a progressive selection of highly specific ligands by performing repeated rounds of partition and amplification from a large combinatorial nucleic acid library. The products of the selection are usually called aptamers, which are short single-stranded deoxyribonucleic acid (ssDNA) or ribonucleic acid (ssRNA) molecules binding with high affinity to a large variety of target analytes. However, SELEX is an iterative process requiring multiple rounds of extraction and polymerase chain reaction (PCR) amplification that demands significant sampling and process time. In order to address these problems, the study presents a new integrated microfluidic system consisting of an automatic SELEX chip and a competitive assay chip to enhance the aptamer screening efficiency. With this approach, an aptamer specific to alpha-fetoprotein (AFP), which is a biomarker for liver cancer, has been successfully screened.