Halpern's research projects have included evaluating cognitive performance of MDMA users and non-users in the Southwest who have not ingested other illegal drugs, and looking at long-term mental function in regular users of ayahuasca. His study into the effects of an experimental treatment giving MDMA to terminally ill cancer patients was shut down due to enrollment challenges after only two subjects had participated. His interest in the use of ergine, psilocybin, and LSD to potentially help relieve cluster headaches led him to recently create the private pharmaceutical company Entheogen Corp, focused on bringing the non-psychoactive LSD analog 2-bromo-LSD (BOL-148) to market as a treatment for cluster headaches.