Many cancers shed malignant cells into the circulation. Albeit their rare frequency, these cancer cells serve both diagnostic and therapeutic purposes. However, their purification, quantification and characterization remain challenging. Here, we present a low-cost, rapid microfluidic cell sorter (μFCS) device for the detection and molecular analysis of circulating tumor cells (CTCs). The μFCS employs a weir-shaped microfluidic structure to separate and capture CTCs from unprocessed whole blood cells based on their size difference. The system further allows on-chip culture and molecular profiling of captured cancer cells, and provides easy cell retrieval for subsequent proteomic and genetic analyses. Using a mouse model of cancer metastasis, we show that the μFCS can enrich CTCs from whole blood to unmask their cancer genetic signature. With its rapid processing speed and versatility for downstream analyses, this platform could have a wide range of potential applications in clinical cancer diagnosis.