With a long history of traditional medicinal use for various ailments including pain relief, Echinacea is currently widely used as an herbal immunomodulator. Despite the popularity of the herb and many pharmacological and clinical studies, it is still uncertain which specific compound(s) are responsible for the reported bioactivities, and the molecular mechanism of action of Echinacea remains poorly understood. Using a combination of HPLC-PDA, GC-MS and HPLC-ESI-MS/MS, we evaluated the phytochemical variation between roots of forty Echinacea accessions with broad geographical and morphological diversity grown under controlled conditions. A dendrogram was generated from these metabolite data and was compared with the two existing taxonomic treatments of the Echinacea genus. We also provided the first examination of the Echinacea-activated calcium-signaling pathway. Three models, rat hippocampal cells, Xenopus laevis oocytes and human HEK293 cells, have been established. Electrophysiological techniques and intracellular calcium imaging were used to study the effect of Echinacea constituents on intracellular Ca²⁺. In all three systems, Echinacea mediates an increase in cytosolic Ca²⁺. In cultured rat astrocytes Echinacea extracts stimulated elevation of cytosolic Ca²⁺ and this activation is related to the CB1 receptor. In frog oocytes, Echinacea-induced current is associated indirectly with transfected TRPV1 pain receptor. Treatment of HEK293 cells with Echinacea extract resulted in an increase in cytosolic Ca²⁺, and investigation of this Ca²⁺ signaling indicated the involvement of PLC activation, IP3 receptor and SOCE pathway. Six bioactive fractions of Echinacea were identified, and metabolite analysis indicates lipophilic constituents are associated with this bioactivity. Interestingly, the constituents thought to be responsible for the major bioactivity of Echinacea (i.e., alkamides/ketones, caffeic acid derivatives) cannot explain the observed shifts in Ca²⁺. So far, the identity of the receptor(s) that bind(s) to Echinacea and activate(s) the observed calcium elevation in HEK293 remains unknown. CB1 and TRPV1 are not involved as neither is present in HEK293 cells. We propose that Echinacea compounds activate specific receptors, including CB1 and TRPV1, in cells of the immune and central nervous system, and perturb intracellular Ca²⁺ signaling, and that this signaling underlies anti-inflammatory and pain-modulating activities of Echinacea.