In this paper, we describe the use of pulsed laser desorption/ionization mass spectrometry (LDI-MS) for the detection of tumor cells through the analysis of gold cluster ions Aun from aptamer-modified gold nanofilms (Au NFs). We observed not only the transformation of the Au NFs into gold nanoparticles (Au NPs) but also the formation of gaseous gold cluster ions (Au(n); n = 1-5) under irradiation with a nanosecond pulsed laser. The size and density of the formed Au NPs and the abundance of Au(n) ions were both highly dependent on the thickness of the Au NFs (10-100 nm). Thin Au NFs tended to form highly dense Au NPs on the substrate and favored the desorption and ionization of gold cluster ions. The signal intensities of the Au(n) species, monitoring using mass spectrometry, decreased upon increasing the thickness of the Au NF from 10 to 100 nm and after modification with thiolated DNA. Furthermore, we found that Au NFs modified with mucin1-binding aptamer (AptMUC1-Au NFs) could selectively enrich MCF-7 cells (human breast adenocarcinoma cell line) in blood samples; coupled with LDI-MS analysis of the Au(n) ions, we could detect MCF-7 cells selectively in blood samples at abundances as low as 10 cells. This approach offers the advantages of high sensitivity, selectivity, and throughput for the detection of circulating tumor cells, and has great potential for use as a powerful analytical platform for clinical diagnoses of tumor metastasis.