They are as follows: Boyle first argued that fire is not a universal and sufficient analyzer of dividing all bodies into their elements, contrary to Jean Beguin and Joseph Duchesne.

Boyle rejected the Aristotelian theory of the four elements (earth, air, fire, and water) and also the three principles (salt, sulfur, and mercury) proposed by Paracelsus.

After discussing the classical elements and chemical principles in the first five parts of the book, in the sixth part Boyle defines chemical element in a manner that approaches more closely to the modern concept: However, Boyle denied that any known material substances correspond to such "perfectly unmingled bodies."

According to E. J. Dijksterhuis, "After the appearance of The Sceptical Chymist Aristotle’s doctrine of the four elements as well as Paracelsus’ theory of the three principia gradually passes into disuse.

"[5] The book's influence can be discerned in Nicholas Brady's reference to "jarring seeds" in his Ode to St. Cecilia (set by Henry Purcell in 1691, well before Daniel Bernoulli's kinetic theory): Philosopher of science Thomas Kuhn references The Sceptical Chymist in the eleventh chapter of his book The Structure of Scientific Revolutions, while discussing his views on the historiography of science.