The last few years have seen a growing interest in the study of the sources and metabolism of isoflavones due to their potential role in the prevention and treatment of chronic disease (i.e., coronary artery disease, osteoporosis, and certain types of cancer). Furthermore, isoflavonoids have reportedly been instrumental in relieving menopausal symptoms (i.e., hot flashes, night sweats, other vasomotor symptoms, and bone loss). Isoflavonoids are compounds that occur naturally in plants and belong to the phytoestrogen family, as do coumestans and lignans. There is much to learn about the effects of isoflavonoids and their potential health benefits; thus they are researched extensively through molecular, preclinical, and clinical studies. Capillary zone electrophoresis (CZE) was explored as a new tool for characterizing the content of isoflavonoids in the urine of subjects who consume large amounts of soy and derivative products. The effect of pH, buffer concentration, and instrument parameters on the migration behavior of these products was studied. Due to the phenolic nature of isoflavonoids, alkaline pHs (8.20-9.90) were tested. The influence of electrolyte concentration in the 50-250 mM range on migration times and resolution was researched. Solid-phase extraction (SPE) was carried out for sample cleanup and preconcentration.