Background: Strychnos nux-vomica is a well-known poisonous plant, which is detoxified by different methods in traditional medicines. Most of traditional medical schools introduce general detoxification methods that can be substituted with each other. The main goal of these methods is to reduce the total alkaloids. In contrast, Iranian traditional medicine (ITM) has suggested three non-general, nonsubstitutable methods, which have specific medical indications: 1, boiling the seeds in water until all the water evaporates (prescribed for diarrhea treatment); 2, soaking the seeds in cow's milk for seven days, followed by peeling the seeds (for addiction treatment); 3, soaking the seeds in cow's milk for seven days, peeling the seeds, and boiling them in milk (for arthralgia and paralysis). Objectives: The aim of this study was to clarify the therapeutic rationale for each method. Materials and Methods: Nux-vomica seeds were divided into four groups: three groups were detoxified via ITM methods, and one group was kept intact as a control. All samples were powdered, and their alkaloids and total phenolic compounds were determined by HPLC and spectrophotometery, respectively. Results: The first ITM method reduced the strychnine level from 1.083 to 0.577 and brucine from 0.739 to 0.361. For the second and third ITM methods, the levels of strychnine reached 0.838 and 0.812, and the levels of brucine reached 0.522 and 0.568, respectively. Conclusions: Clinically, these results are logical because the required dose of alkaloids for treatment of diarrhea is lesser than the needed doses to treat addiction, arthralgia, and paralysis.