When the Aplysia ELH precursor is expressed in AtT-20 cells, the carboxyterminal derived peptides are packaged and stored in secretory vesicles, while the aminoterminal region of the precursor is constitutively secreted. In contrast, when the highly homologous A peptide precursor is transfected into AtT-20 cells, both aminoterminal and carboxyterminal derived peptides are packaged in storage granules. We propose that this is due to the fact that the initial cleavage of the A peptide precursor occurs more slowly, and perhaps later in the secretory pathway, than the ELH precursor. We further suggest that in the A peptide precursor, the first cleavage occurs after the sorting site resulting in co-packaging of the multiple products derived from a single precursor protein. To determine the structural features of the prohormones responsible for this differential sorting, we made chimeric precursors and determined the rates of the initial cleavage as well as the efficiency of storing the peptide products. From these studies, we conclude that the differential sorting is regulated both by the amino acid sequence of the first processing site, and by more global aspects of the precursor structure.