Double negations are easily recognised in both the so-called “negative literature” and the original texts of some important scientific theories. Often they are not equivalent to the corresponding affirmative propositions. In the case the law of double negation fails they belong to non-classical logic, as first, intuitionist logic. Through a comparative analysis of the theories including them the main features of a new kind of theoretical organization governed by intuitionist logic are obtained. Its arguing proceeds through doubly negated propositions and ad absurdum arguments. Then, the final doubly negated predicate is translated in the corresponding affirmative one, from which all the consequences are deduced in order to test them against reality. According to this model the true formalization of intuitionist logic is Kolmogorov’s 1932 paper. The above analysis also shows that modal words play an auxiliary or substitutive role to intuitionist propositions. In addition, it is shown that Vasiliev’s paraconsistent logic is represented through doubly negated propositions. By means of these three kinds of logic one can attribute a specific kind of logic to each of the three distinct steps of the process of building a scientific theory from the experimental data to its final theoretical system. It is also shown that the definition of negation is of a structural kind, rather than of an objective kind or a subjective kind: it has to be referred to the organization of the theory to which it belongs.