Cuttlebone is a natural material possessing a unique microstructure providing a high compressive strength to weight ratio. It is potentially desirable to use cuttlebone directly in engineering applications or to design new biomimetic materials based on the microstructural features of cuttlebone. A finite element based homogenization method can be used for characterizing the mechanical properties of such a biomaterial and for the design of biomimetic materials. However, this method assumes a periodicity of microstructure, which does not reflect the variation present in natural or fabricated materials. The method can be extended to investigate the effect of natural variation and manufacturing tolerance by enlarging the base cell domain to include a number of representative volume elements (RVEs) and applying a random displacement vector to the nodes at the internal intersections of the RVEs. As the boundary of the base cell domain is not modified, the homogenization method can still be employed to calculate the bulk mechanical properties. It is found that the number of RVEs in the base cell has an impact on the decrease in mean stiffness tensor components, while the length of the introduced variation seems to influence both the mean and the standard deviation of stiffness tensor components.