Detecting and analyzing circulating tumor cells (CTCs) in the blood of cancer patients is a promising approach for the early diagnosis of metastasis. Previously, we developed a size-selective filter for capturing CTCs, but its use was time consuming, particularly for capturing CTCs from large volumes of blood. In the present study, we describe the use of a magnetic capture column for rapid and efficient isolation of CTCs, which were magnetically labeled with magnetite cationic liposomes. In the capturing process, large volumes of blood containing magnetically labeled cancer cells were introduced into the column at a high flow rate to capture the cells, which were then added into the filter at a low flow rate. Our results show that the combined use of the column and filter decreased the required time for the spiked cancer cell capture, and the recovery rate of the spiked cancer cells from blood was significantly higher using the combination process (80.7 %) than that using the filter alone (64.7 %). Moreover, almost twice the number of CTCs could be captured from the blood of metastatic model mice using the combination process. These results suggest that the developed process would be useful for the rapid and efficient isolation of CTCs.