Nanoscale objects with advanced structure and function are of considerable interest in areas such as sensing, drug delivery and bioelectronics, [1,2] and have important implications for biotoxicity [3,4] and the emergence of life. [5] In many cases, the synthesis and structuration of hybrid nano-objects is achieved under equilibrium or non-equilibrium conditions through a range of strategies involving integrative, higher-order, or transformative self-assembly. [6,7] Often these approaches involve the confinement and templating of reactions on or within supramolecular assemblies such as dendrimers, [8] organogel nanofilaments, [9] peptide fibers, [10] helical micelles, [11] virus capsids, [12] and protein cages. [13] Recently, cross-linked lysozyme crystals, approximately 200 mm in size, have been used to prepare nanoplasmonic arrays by intracrystalline metallization, [14] suggesting that the high mesoporosity of protein crystals might be exploited in general for the template-directed assembly of organized inorganic nanostructures across a range of length scales. Whilst many common proteins readily form crystals with macroscopic dimensions, it is generally difficult to produce nanoscale counterparts that would be effective as templates for the preparation of discrete hybrid nanomaterials. In this regard, the iron storage protein, ferritin, which consists of a 12 nm diameter spherical polypeptide shell enclosing a 5-6 nm sized iron oxide core [15] is known to readily form two-dimensional (2D) superlattices on various substrates [16] and can be clustered into aggregates in solution using biotin-streptavidin linkages or inorganic nanoparticles.[17] It should therefore be possible to control the self-assembly of discrete nanometersized ferritin crystals, and as a consequence use these nanocrystals as porous templates for the fabrication of hybrid nanoparticles with ordered mesostructured interiors.Here, we use water-in-oil microemulsion droplets as a medium for controlling the aggregation of entrapped ferritin molecules to produce discrete protein nanocrystals that can be stabilized by in situ silicification of the intracrystalline voids to produce mesostructured silica-ferritin hybrids. Microemulsions are versatile reaction media for the confinement and synthesis of inorganic nanoparticles, [18] nanowires, [19] nanoparticle superlattices, [20] and complex hierarchical architectures.[21] In addition, microemulsion droplets have been used for the encapsulation of drugs, [22] exploration of organic chemical reactions, [23] entrapment of functional enzymes, [24] and for the separation of protein mixtures.[25]Although droplet instability can often be a problem in these applications, herein we demonstrate that protein-mediated aggregation of the water pools can be exploited to produce discrete ferritin nanocrystals and silicified counterparts with well-ordered close packed structures. As silicification of the interstitial pores occurs with high precision and without degradation of the protein, it should be possible to ex...