In the frame of a statistical tolerance analysis of complex assemblies, for example an aircraft wing, the capability to predict accurately and fast specified, very small quantiles of the distribution of the assembly key characteristic becomes crucial. The problem is significantly magnified, when the tolerance synthesis problem is considered in which several tolerance analyses are performed and thus, a reliability analysis problem is nested inside an optimisation one in a fully probabilistic approach. The need to reduce the computational time and accurately estimate the specified probabilities is critical. Therefore, herein, a systematic study on several state of the art simulation methods is performed whilst they are critically evaluated with respect to their efficiency to deal with tolerance analysis problems. It is demonstrated that tolerance analysis problems are characterised by high dimensionality, high non-linearity of the state functions, disconnected failure domains, implicit state functions and small probability estimations. Therefore, the successful implementation of reliability methods becomes a formidable task. Herein, advanced simulation methods are combined with in-house developed assembly models based on the Homogeneous Transformation Matrix method as well as off-the-self Computer Aided Tolerance tools. The main outcome of the work is that by using an appropriate reliability method, computational time can be reduced whilst the probability of defected products can be accurately predicted. Furthermore, the connection of advanced mathematical toolboxes with off-the-self 3D tolerance tools into a process integration framework introduces benefits to successfully deal with the tolerance allocation problem in the future using dedicated and powerful computational tools.