Freethinkers strive to form their opinions on the basis of facts and reason. An idealized statement of this attitude is "Clifford's Credo," an aphorism of the 19th Century British mathematician and philosopher William Kingdon Clifford who wrote in his "Ethics of Belief" that "It is wrong always, everywhere, and for anyone, to believe anything upon insufficient evidence." Because so many popular beliefs are based on tradition or authority, freethinkers' opinions are often at odds with established dogmatic, political, social, intellectual or religious views. Many freethinkers, although by no means all, believe that there is insufficient evidence to support the existence of such supernatural entities and phenomena as ghosts, gods, angels, devils, leprechauns, reincarnation, heaven, hell, and so on. In Western society, freethought often involves a rejection of Christianity, or indeed of any religious doctrine. This rejection itself may arise from dogmatically held prejudice, and a true freethinker will be on guard against such prejudgements. Where other dogmas or doctrines are prevalent, those who dissent from them on the basis of facts and rational analysis also exhibit the principles of freethought. This will apply regardless of what the prevailing or approved doctrine might be, whether religious or not.

There are often ties between freethought and atheism, agnosticism, deism, heresy, skepticism (scepticism), and both humanism and secular humanism, but none of these terms are synonymous with one another nor are their referents necessarily compatible with freedom of thought. Even Freethought is used to refer to different things by different people. An orthodox believer in any faith, for example, may be a freethinker if he or she has come to accept those beliefs on the basis of reason, if they question and/or reject one or more articles of their religion's doctrines, or if they have rejected alternative beliefs on the basis of free and rational thought in accordance with reason. Deists claim that they can know that a deity exists through rational argument which demands the existence of a first cause.

"Clifford's Credo" and the writings of many freethinkers indicate that nonreligious thought can have moral foundations as strong as those found in religious traditions.

Some atheist freethinkers hold that freethought may be considered a religion itself, or at least as a form of religious philosophy, since it offers alternative analyses of and conclusions about religious questions which do not include supernaturalism. In 1994, this idea was acted on in the founding of the Church of Freethought, which now exists as two active congregations of freethinkers: the North Texas Church of Freethought and the Houston Church of Freethought.