Enamel matrix comprises nanospheres predominantly composed of amelogenin. Studies have shown that recombinant amelogenin forms nanospheres similar to those formed in vivo, but it is unclear exactly how nanospheres assemble in vivo. Are amelogenin monomers secreted into the enamel matrix where they then self-assemble to form nanospheres, or does nanosphere assembly actually occur intracellularly? The aim of this study was to attempt to answer this question. Rat enamel organs were treated with the bifunctional cross-linker, dithio bis (succinimidyl propionate) (DSP), which cross-links primary amines lying in close molecular proximity. The key to this technique is the fact that DSP cross-links are later sensitive to reductive cleavage. The cross-linked proteins were first subjected to non-reducing sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE) in the first dimension and then to reducing SDS–PAGE in the second dimension (so-called diagonal electrophoresis) followed by western blot probing with anti-amelogenin. The results indicated that intracellular amelogenin monomers are in close neighbor contact, forming complexes comprising up to six individual amelogenin monomers. We suggest that these initial complexes are prefabricated intracellularly before secretion. Once secreted, these prefabricated subunits assemble further to form the mature full-size nanospheres containing hundreds of individual amelogenins characteristic of enamel matrix.