To select the optimal therapeutic strategy for individual patients with cancer, clarification of the biological behaviorof the tumor using minimal invasive methods is necessary. Circulating tumor cells (CTCs) and circulating cell-free DNA (ctDNA) released into the bloodstream from the primary tumor and metastases reflect the current tumor status. To establish a noninvasive method for identifying mutation status in tumor cells, we tried to develop methods for next-generation sequencing (NGS) from CTCs and ctDNA. CTCs were isolated using a cascading spiral system with patient blood (Hou et al, Scientific Rep. 2013) while ctDNA and DNA extracted from CTCs were analyzed by NGS (Ion PGM; LifeTechnology). Thirty-four patients with gastric, colorectal, esophageal, or head and neck cancers were enrolled in this study. A total of 8-77 CTCs/ml were retrieved from whole blood. Mutation profiles were successfully identified from CTCs and ctDNA obtained from each patient by NGS.