Batten disease or neuronal ceroid lipofuscinoses (NCL) are a group of genetic neurodegenerative diseases that primarily afflict infants and children and are characterized by progressive loss of brain functions caused by the death of central nervous system (CNS) neurons. The most severe form of the disease is infantile NCL (INCL). INCL is caused by mutations in the palmitoyl-protein thioesterase 1 (PPT1) gene, which encodes a palmitoyl-protein thioesterase 1 enzyme that cleaves long-chain fatty acids from S-acylated proteins within the lysosome. How the loss of this activity causes the death of CNS neurons is not known. A PPT1 homolog and palmitoyl-protein thioesterase 1 enzyme activity were characterized in Drosophila melanogaster as an initial step in developing Drosophila as a model system for studying the etiology of INCL. Predicted gene CG12108 in region 8A2 of the X chromosome is 55% identical and 72% similar to human PPT1 and contains conserved catalytic residues and sites of glycosylation. Northern-blot hybridizations revealed a major 1.5 kb CG12108 transcript in unfertilized eggs, embryos, larvae, pupae, adult head and thorax, ovary, testis, and S2 tissue culture cells, as well as several minor mRNA species in some tissues. Levels of the 1.5 kb transcript were fairly uniform among tissues except in testis, where the transcript was enriched 5-fold. The same tissues also contained palmitoyl-protein thioesterase 1 enzyme activity measured using the fluorometric substrate 4-methylumbelliferyl-6-thiopalmitoyl-beta-D-glucoside. Enzyme activity was highest in testis and varied among the other tissues to a greater extent than did CG12108 message, suggesting that CG12108 is subjected to post-transcriptional regulation. Finally, flies homozygous for a deletion that removes CG12108 and three unrelated neighboring genes had less than 3% of wildtype levels of enzyme activity, consistent with CG12108 encoding functional palmitoyl-protein thioesterase 1 activity and being the fly ortholog of human PPT1. CG12108 has been appropriately renamed Ppt1.