Presence of circulating tumor cells (CTCs) in blood is an important intermediate step in cancer metastasis, a mortal consequence of cancer. However, CTCs are extremely rare in blood with highly heterogeneous morphologies and molecular signatures, thus making their isolation technically very challenging. In the past decade, a flurry of new microfluidic-based technologies has emerged to address this compelling problem. This chapter highlights the current state of the art in microfluidic systems developed for CTCs separation and isolation. The techniques presented are broadly classified as physical- or affinity-based isolation depending on the separation principle. The performance of these techniques is evaluated based on accepted separation metrics including sensitivity, purity and processing/analysis time. Finally, further insights associated with realizing an integrated microfluidic CTC lab-on-chip system as an onco-diagnostic tool will be discussed.