Technical Abstract: As a modern analytical technique, capillary electrophoresis (CE) has become an attractive method for characterizing molecules wit high structural complexity and a wide range of molecular weights. CE can be used to analyze many natural chemical components such as acids, biogenic amines, peptides, proteins, DNAs, carbohydrates, phenols, polyphenols, pigments, toxins, pesticides, vitamins, small organic and inorganic ions, and chiral compounds. To promote broader applications of CE technology in agricultural and soil chemistry studies, this chapter reviews, as case studies, the research in CE characterization and quantification of cotton physiological (developmental) enzyme and protein products, cottonseed ingredient gossypol, and soil humic acids. Monitoring changes of three pectin-degrading enzyme activities reveals the possible involvement of these enzymes in cotton cotyledon expansion. CE measurement of cottonseed ingredient gossypol with or without post-column chemiluminecence reaction provides an alternative for rapid determination of gossypol in cottonseed and other biological samples. This chapter details the CE profiles of the International Humic Substances Society (IHHS) humid substances and the mobile humic acid (MHA) and recalcitrant calcium humate (CaHA) fractions extracted from Philippine rice soils and Nebraska (USA) corn soils under different fertilizer managements. These studies demonstrate that CE could contribute to a better understanding of agricultural and soil chemistry for crop growths, products, and nutrients.