The paper presents an advanced stiffness modeling technique for perfect and non-perfect parallel manipulators under internal and external loadings. Particular attention is paid to the manipulators composed of non-perfect serial chains, whose geometrical parameters differ from the nominal ones and do not allow to assemble manipulator without internal stresses that considerably affect the stiffness properties and also change the end-effector location. In contrast to other works, several types of loadings are considered simultaneously: an external force applied to the end-effector, internal loadings generated by the assembling of non-perfect serial chains and external loadings applied to the intermediate points (auxiliary loading due to the gravity forces and relevant compensator mechanisms, etc.). For this type of manipulators, a non-linear stiffness modeling technique is proposed that allows to take into account inaccuracy in the chains and to aggregate their stiffness models for the case of both small and large deflections. Advantages of the developed technique and its ability to compute and compensate the compliance errors caused by the considered factors are illustrated by an example that deals with parallel manipulators of the Orthoglide family.