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The therapies and philosophy on which naturopathic medicine is based can be traced back to the ancient healing arts of early civilizations. Healers in ancient times used natural treatments that relied on the body's innate ability to heal itself. They made use of foods, herbs, water, massage, and fasting.

Hippocrates, who is thought by many to be the father of modern medicine, is also often considered to be the earliest predecessor of naturopathic physicians. He used many natural approaches to health care. He is reported to have told his followers, "Let your food be your medicine and your medicine be your food."

During the 18th and 19th centuries, an alternative healing movement in Europe contributed to the development of naturopathic medicine. The German homeopathic practitioner John H. Scheel is credited with first using the term "naturopath" in 1895.

Dr. Benedict Lust introduced naturopathy to the United States. He founded the American School of Naturopathy, which graduated its first class in 1902. In 1909, California became the first state to legally regulate the practice of naturopathy. Early naturopaths, including Dr. John Kellogg, his brother Will Kellogg, and C. W. Post, helped popularize naturopathy.

Naturopathy flourished in the early part of the 20th century. By 1930, there were more than 20 naturopathic schools and 10,000 practitioners nationwide. With the rise of modern pharmaceuticals and allopathic (conventional) medicine, naturopathic medicine experienced a decline during the 1940s and 1950s. The latter part of the 20th century, however, saw a strong revival in the field of naturopathy due to rapidly growing public interest in alternative health care approaches. One sign of the importance of alternative medicine was the founding in 1992 of the Office of Alternative Medicine (OAM) as part of the National Institutes of Health. The OAM's responsibilities included evaluating treatments and providing information to the public about them. In 1999 the OAM became the National Center for Complementary and Alternative Medicine (NCCAM), with greater access to resources for initiating and funding additional research projects. In December of 2014 Congress renamed NCCAM once again, and the organization became the National Center for Complementary and Integrative Health (NCCCIH). In 2020 NCCIH continued to conduct important research, with funding of $151.9 million and the equivalent of 68 full-time employees.