Joseph Amalfitano graduated from South Lake High School in St. Clair Shores Michigan in 1982 and subsequently attended Eastern Michigan University for 1 year. After transferring to the University of Michigan in 1983, he received a bachelors degree in Microbiology and was accepted to the dental school also at the University of Michigan in 1986. During his training, he participated in various research projects and studied the microbiology of periodontal disease.