Part tolerances and fixture layouts are two pivotal factors in the geometrical quality of a compliant assembly. The independent design and optimization of these factors for compliant assemblies have been thoroughly studied. However, this paper presents the dependency of these factors and, consequently, the demand for an integrated design of them. A method is developed in order to address this issue by utilizing compliant variation simulation tools and evolutionary optimization algorithms. Thereby, integrated and non-integrated optimization of the tolerances and fixture layouts are conducted for an industrial sample case. The objective of this optimization is defined as minimizing the production cost while fulfilling the geometrical requirements. The results evidence the superiority of the integrated approach to the non-integrated in terms of the production cost and geometrical quality of the assemblies.