Multifunctional materials are created by intimately integrating different materials. The assessment of the local properties and composition of the different components of such a multifunctional material necessarily relies on techniques with sufficient spatial resolution. The increased use of these microanalysis or microprobe techniques has created a demand for appropriate quality assurance tools, such as reference materials. In this paper a number of issues related to the certification of reference materials for multifunctional materials are discussed. Examples of reference materials are shown to illustrate the particular challenges the reference material producer is faced with such as micro-homogeneity, minimum sample intake and stability.