Molecular characterization for circulating tumor cells (CTCs) can be used to better understand the biology of metastasis, to improve patient management and help to identify novel targets for biological therapies aimed to prevent metastatic relapse. New areas of research are directed towards developing novel sensitive assays for CTC molecular characterization. Towards this direction, molecular detection technologies that take advantage of the extreme sensitivity and specificity of PCR, offer many advantages, such as high sensitivity, specificity, and significant flexibility in the clinical lab setting, in terms of high-throughput analysis, multiplexing, and quality control issues. Using molecular assays, a variety of molecular markers such as multiple gene expression, DNA methylation markers, DNA mutations, and miRNAs have been detected and quantified in CTCs in various cancer types, enabling their molecular characterization. Here, we present the main molecular detection technologies currently used for CTC analysis and molecular characterization.