In this study, we have analyzed the chemical composition and antiproliferative activity of propolis from three different arid and semiarid regions of Sonora, Mexico. We identified and quantitated the main chemical constituents of propolis by HPLC-MS. The most abundant constituents of propolis were pinocembrin, pinobanksin 3-acetate, and chrysin. Sonoran propolis had a strong antiproliferative activity on both murine and human cancer cell lines in a concentration-dependent manner. The propolis constituents CAPE, galangin, xanthomicrol and chrysin showed significant antiproliferative activity on most of the cancer cells tested. DNA harvested from cancer cell cultures treated with Sonoran propolis exhibited a ladder of internucleosomal DNA cleavage characteristic of apoptosis. In summary, we have identified and quantitated the main constituents of Sonoran propolis. These propolis samples possess a strong antiproliferative activity on cancer cell lines.