The method of the joint probability distribution functions of structure factors has been extended to reflections with rational indices. The most general case, space group P1, has been considered. The positional parameters are the primitive random variables of our probabilistic approach, while the reflection indices are kept fixed. Quite general joint probability distributions have been considered from which conditional distributions have been derived: these proved applicable to the accurate estimation of the real and imaginary parts of a structure factor, given prior information on other structure factors. The method is also discussed in relation to the Hilbert-transform techniques.