Born’s probabilistic interpretation of quantum mechanics is commonly assumed to rely on classical probability theory in the sense of Kolmogorov. In this paper we argue that this assumption is methodologically unjustified. We show that quantum probabilities naturally arise from an analytic method fundamentally different from the synthetic approach underlying classical probability theory. In the analytic framework, the whole (the totality of alternatives) is primary, while probabilities of individual alternatives are derived quantities. Interference appears at the level of the realization probability of the whole, whereas conditional probabilities of alternatives remain additive within a given context. We demonstrate that many well-known quantum paradoxes originate from the inappropriate application of synthetic probabilistic reasoning. The proposed formulation is consistent with the Born rule, its extensions developed in our earlier works, and with Birkhoff–von Neumann quantum logic. Classical probability theory appears only as a degenerate formal limit and is not methodologically universal.