Experiments form a key part of The New Organon. They are used to investigate nature, and to show how things perform in an unknown situation. This represents a major difference between Bacon and earlier scientific thinkers, who generally used experiments (or thought-experiments) to confirm a previously-held theory.

For Bacon, this is a ridiculous notion. Theories can come only from practical experiments and experience of nature. The second book of The New Organon details many experiments performed by Bacon and his assistants and describes the use of scientific instruments such as the microscope. Lisa Jardine links Bacon to contemporary experimenters such as Gilbert and William Harvey, who discovered the circulation of the blood, and sees him as a predecessor of scientists like Boyle and Hooke. Bacon's emphasis on experiments was perhaps fatal; one account of his death claims that it resulted from catching cold after stuffing a chicken with snow to investigate freezing.