The book's argument begins where Eddy's own account of her life turns: her recovery in 1866, after a severe fall in Lynn, Massachusetts, while reading an account of one of Jesus's healings, an experience she spent the following years working into a system. Science and Health presents that system in chapters on prayer, atonement and eucharist, marriage, spiritualism contrasted and rejected, science and theology and medicine, physiology, and the interpretation of Genesis and the Apocalypse that gives the book the second half of its title.
The core positions are stated without compromise. God is All-in-all, infinite Mind, and matter possesses no true life, substance or intelligence; the human condition described by the senses, including disease, is a misapprehension that yields to the understanding of God's allness, as shadow yields to light. Healing therefore is not miracle and not willpower but the operation of divine law, repeatable in principle by anyone, which is why Eddy called the teaching a science.
The chapter Recapitulation, arranged as questions and answers, condenses the doctrine for teaching and includes the statement of being that begins there is no life, truth, intelligence, nor substance in matter. A glossary assigns spiritual senses to biblical names, and the closing chapter, Fruitage, prints firsthand accounts of readers who report recovery from long illness through study of the book alone.