A method for identification of circulating tumor cells (CTCs) in a blood sample uses magnetic enrichment and a nanowell assay. The CTCs are magnetically labeled with cancer cell markers conjugated to magnetic nanoparticles and then separated by passing the blood sample through a magnetic sifter. The enriched CTCs are then loaded into a microfluidic single-cell molecular assay comprising an array of 25,600 or more nanowells, each containing at most a single one of the CTCs. Using multiple fluorescent gene markers, simultaneous multiple-color multiplexed gene expression of the CTCs is performed, preferably using RT-PCR. Images of fluorescence signals from individual nanowells are analyzed to identify CTCs.