We present a high-throughput screening Raman spectroscopy (HTS-RS) platform for a rapid and label-free macromolecular fingerprinting of tens of thousands eukaryotic cells. The newly proposed label-free HTS-RS platform combines automated imaging microscopy with Raman spectroscopy to enable a rapid label-free screening of cells and can be applied to a large number of biomedical and clinical applications. The potential of the new approach is illustrated by two applications: 1. HTS-RS-based differential white blood cell count. A classification model was trained using 52218 Raman spectra of lymphocytes, 48220 spectra of neutrophils and 7294 spectra of monocytes from four normal volunteers. The model was applied to white blood samples of two volunteers and three patients, with comparable results for white blood cell counts between HTS-RS and machine counting. 2. HTS-RS-based identification of circulating tumour cells (CTCs) in 1:1, 1:9 and 1:99 mixtures of Panc1 cells and leukocytes yielded ratios of 55:45, 10:90 and 3:97, respectively.