Analysis of the enamel matrix during porcine tooth formation has revealed a number of high molecular-weight (Mr) enamel proteins (greater than 30 kDa), which are related to the major amelogenins (20-26 kDa). To examine the nature of these proteins, amelogenins were extracted and separated by conventional gel filtration and reverse phase HPLC. Many of the proteins in the high Mr fraction reacted with a polyclonal antibody, affinity-purified against a mixture of 20-26 kDa amelogenins. Another antibody, affinity-purified against a fraction containing the LRAP, reacted with amelogenins 30-36 kDa in size but not with amelogenins 40 kDa or larger, indicating that the high Mr amelogenins were a heterogeneous group of enamel proteins. Analysis of amino acid composition and N-terminal amino acid sequence, as well as PASGE of electrophoretically eluted proteins, indicated that the high Mr amelogenins were aggregates of various major amelogenins. Three amelogenin aggregates (43, 40 and 32 kDa) isolated by electrophoretic elution were less stable at 100 degrees C in SDS-containing buffer than at 60 degrees C. In contrast to the major amelogenins, which are found in constant proportions throughout enamel development, the high Mr amelogenins appeared to increase in maturing enamel relative to the total matrix protein. Thus, at least in the pig high Mr amelogenins appear to be naturally occurring, stable aggregates of major amelogenins. It is proposed that amelogenin aggregation occurs as a consequence of the diminishing spaces between growing crystals in maturing enamel.