Wiley's main thesis in Lights Out is that light is a physiological trigger that controls dopamine and hormones like cortisol. Wiley posits that with the extension of the natural day through artificial lighting, rest at the hormonal level is rarely adequate for optimum biological needs of the body. In her view, this results in both fatigue and unnatural appetite, which leads to weight gain, exhaustion and disease. Wiley theorizes that the body's responses are cyclical, reflecting the seasons of the year, and that the body's needs vary seasonally. According to Wiley, during the winter months the body needs more sleep, and carbohydrates should be restricted as they would have been naturally during hunter-gatherer times.

Wiley is listed as co-author of three scientific journal articles along with biochemist Dr. Bent Formby between 1998 and 2001.

The Wiley Protocol

In her follow-up book, Sex, Lies and Menopause, Wiley theorizes that imbalances in hormones such as estrogen, progesterone, insulin, cortisol, and prolactin, among others, are the root cause of age-related diseases including cancer, heart disease, diabetes mellitus, stroke, and Alzheimer's. These imbalances, Wiley claims, can be attributed to deviations from humankind's natural state—artificial light, sleeping too much in the summer and not enough during winter, and eating fruit during winter months—and indirectly to women's liberation, insofar as it has led to the increased use of contraceptives, deferral of child bearing into the 20s and 30s, less frequent childbirth, and reduced breastfeeding. Wiley's Protocol attempts to mimic the youthful levels and cycles of estrogen and progesterone in order to prevent or treat age-related diseases. Wiley believes conventional hormone replacement therapy is ineffective and dangerous, advocating instead rhythmic, cyclical dosing of bioidential hormones.

Subsequent to the book's publication, her hormone regimen became known as the "Wiley Protocol." Wiley created a registered pharmacy program to ensure the consistency of the compounded products. Pharmacists enter a contract stipulating compounding methods, materials, testing, packaging and recommended pricing while Wiley's company provides the packaging materials bearing the Wiley Protocol trademark. Training for pharmacists is handled by a third party. Wiley offers educational courses for physicians for which they receive CME credits. Suzanne Somers advocates the Wiley Protocol in her book Ageless: The Naked Truth About Bioidentical Hormones.

Wiley has been criticized for promoting her version of BHRT without proper qualifications or scientific evidence. On October 11, 2006, Erika Schwartz, Diana Schwarzbein, and five other MDs who have worked with BHRT during their careers issued a public letter to Suzanne Somers and her publisher, Crown, criticizing Somers' endorsement of Wiley's protocol. In the letter they alleged that the Wiley Protocol is "scientifically unproven and dangerous" and that Wiley has no medical or clinical qualifications; other criticisms of the protocol itself have stated that the levels of hormone are dangerously high. Wiley has claimed on her website and in speaking engagements that she earned a B.A. in anthropology from Webster University in 1975. On November 27, 2006, Newsweek reported that Webster has no record of this degree. Wiley's bio page was then changed to "Pending B.A. in Anthropology, Webster University, 1975" and then again to "Attended the B.A. Program in Anthropology, Webster University, 1970-1975". ABC News reported on February 16, 2007, that, according to Webster, she received only a blank diploma.

On April 19, 2007, Wiley appeared as a witness before the Senate Special Committee on Aging to give testimony at a hearing in which the safety and oversight of BHRT and compounding pharmacy were discussed.