Inner product mapping (IPM) has been proposed as a hybridization-based method for achieving low-cost, high-throughput, high-resolution radiation hybrid (RH) mapping of clones. Using Alu-PCR products of chromosome 11-specific clones, we serially hybridized a set of RHs against gridded filters of YACs having an average size of 350 kb. We then combined these hybridization data with preexisting RH map data to build an inner product map. This binning of 865 YACs provides the first high-resolution large-scale (> twofold redundancy) clonal coverage of human chromosome 11 and is the first inner product map ever constructed. We verified the accuracy and precision of this chromosome 11 map by performing a novel likelihood analysis on independent YAC hybridization data. These results establish that IPM is a highly rapid, inexpensive, accurate, and precise large-scale long-range mapping method, particularly when preexisting RH maps are available, and that IPM can replace or complement more conventional short-range mapping methods. IPM may enable the rapid construction of sequence-ready maps and the binning of expressed sequences.