Secretory polypeptides are vital for nervous system function, sleep, reproduction, growth, and metabolism. Ribosomes scanning the 5'-end of mRNA usually detect the first AUG site for initiating translation. The nascent propeptide chain is then directed via a signal-peptide into the endoplasmic reticulum, processed through the Golgi stacks, and packaged into secretory vesicles. By expressing prepropeptide-EGFP fusion proteins, we observed unusual destinations, mitochondria, nucleus, and cytoplasm, of neuropeptide Y (NPY), atrial natriuretic peptide, and growth hormone in living murine cardiac cells and hypothalamic slices. Subcellular expression was modulated by Zn++ or mutations of N-terminal prohormone sequences but was not due to overexpression in the trans-Golgi network. Mitochondrial targeting of NPY also occurred without the EGFP tag, was enhanced by site-directed mutagenesis of the first AUG initiation site, and abolished by mutation of the second AUG. Immunological methods indicated the presence of N-terminal truncated NPY in mitochondria. Imaging studies showed depolarization of NPY-containing mitochondria. P-SORT software correctly predicted the secondary intracellular destinations and suggested such destinations for many neuropeptides and peptide hormones known. Thus, mammalian cells may retarget secretory peptides from extracellular to intracellular sites by skipping the first translation-initiation codon and thereby alter mitochondrial function, gene expression, and secretion.