This paper presents a novel tolerance analysis method for the photonic assembly domain. It systematically links the characteristics of microfabrication technology to optical coupling. A package design is described by physical tolerance elements, each one representing a specific microfabrication step. Mathematical tolerance elements are added to complete the package description. When error distributions are added to the physical tolerance elements, an optical coupling expectancy of a package design can be obtained. Moreover, it is demonstrated how this method can be used to characterize the contribution of individual design and fabrication factors to the total alignment performance. The tolerance analysis method is generic in nature since it makes use of elementary and generic fabrication steps. The main benefits of the method are its systematic approach, the insight it gives in the performance of a design as well as the major factors affecting the performance, and the analysis of design variations it allows.