Monoclonal antibodies (mAbs) have been widely used to probe molecular components of specific cell types or cellular structures. We have developed a method to enrich antigens of low abundance in heterogeneous molecule mixtures by subtracting abundant antigens. The subtracted immunogen mixture is then used for immunization, which significantly increases the production of mAbs that exhibit specific staining patterns. By applying this "antigen subtraction" method to the embryonic extract of Caenorhabditis elegans, we have successfully isolated 35 mAbs that recognize specific structures, including P granules, muscles, the pharynx, and subsets of hypodermal cells; some of the mAbs revealed previously unreported cellular structures. This antigen subtraction approach can be used in various applications to produce mAbs against relatively scarce antigens in complex molecular mixtures. The mAbs will be useful tools for developmental and cell biological studies.