CancerLocator is a software package for non-invasive cancer diagnosis using methylation profiles of cell-Free DNA. It exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data.CancerLocator is implemented in Java and is freely available on GitHub under the MIT license. The source code is also available at Zenodo (DOI: 10.5281/zenodo.375649).