We evaluated the pharmacological consequences of tissues other than crown being included with harvested peyote. Mean mescaline concentrations were determined for crown, non-chlorophyllous stem, and root, using mature individuals from the same population in South Texas. Samples of each tissue—crown, non-chlorophyllous stem, and root—were taken from each of 13 individual plants. Samples were dried, triturated, defatted, and extracted with methylene chloride, using an acid-base aqueous wash to recover the alkaloids. The concentration of mescaline in each sample was determined by HPLC. The average mescaline concentration in non-chlorophyllous stem was an order of magnitude lower than that in crown, whereas the mescaline concentration in root was two orders of magnitude lower than that in crown. These results show that non-chlorophyllous stem is a poor source of mescaline, and root is an extremely poor source. These results have important implications for conservation, suggesting that non-traditional harvesting of peyote for religious or medicinal use involving the cutting of non-chlorophyllous tissue are contributing to the death of plants and the subsequent failure to regenerate new crowns. Therefore, this practice should be reevaluated by peyote harvesters and users.