Capture-C is a member of the chromosome-conformation-capture family of experimental methods which probes the 3-D organisation of chromosomes within the cell nucleus. It provides high-resolution information on the genome-wide chromatin interactions from a set of target genomic locations, and is growing in popularity as a tool for improving our understanding of cis-regulation and gene function. Yet, analysis of the data is complicated, and to date there has been no dedicated or easy-to-use software to automate the process. We present capC-MAP, a software package for the analysis of Capture-C data.