Biogenesis of lysosome-related organelles complex-1 (BLOC-1) is a protein complex involved in the formation of endosomal tubular structures that mediates the sorting of protein cargoes to specialised compartments. In this study, we present insights into the metabolic consequences caused by BLOC-1 deficiency in pallid mice, which carry a null mutation in the Bloc1s6 gene encoding an essential component of this complex. The metabolome of the hippocampus of pallid mice was analysed using an untargeted, liquid chromatography-coupled mass spectrometric approach. After data pretreatment, statistical analysis and pathway enrichment, we have identified 28 metabolites that showed statistically significant changes between pallid and wild-type control. These metabolites included amino acids, nucleobase-containing compounds and lysophospholipids. Interestingly, pallid mice displayed increased hippocampal levels of the neurotransmitters glutamate and N-acetyl-aspartylglutamic acid (NAAG) and their precursor glutamine. Expression of the sodium-coupled neutral amino acid transporter 1 (SNAT1), which transports glutamine into neurons, was also upregulated. Conversely, levels of the neurotransmitter precursors phenylalanine and tryptophan were decreased. Interestingly, many of these changes could be mapped to overlapping metabolic pathways. The observed metabolic alterations are likely to affect neurotransmission and neuronal homeostasis and in turn could mediate the memory and behavioural impairments observed in BLOC-1-deficient mice.The pallid (pa) mouse, originally called pinked-eyed 2, was isolated based on abnormal coat and eye colour 1 . The defective gene was identified by positional cloning and found to encode a small, coiled-coil-forming protein, named pallidin (also known as biogenesis of lysosome-related organelles complex 1 subunit 6, BLOC1S6) 2 . Besides the pigmentation defect, the pallid mouse was found to display platelet storage pool deficiency and emphysematous lung lesions. This led to the proposal that it would serve as a model for Hermansky-Pudlak syndrome (HPS) 3 . In fact, at least two HPS patients were found to carry recessive mutations in the human pallidin-encoding gene, BLOC1S6 (formerly known as PLDN), thereby defining HPS type 9 (HPS-9) 4 .Pallidin is part of the biogenesis of lysosome-related organelles complex 1 (BLOC-1), which also includes the proteins dysbindin, muted, cappuccino, snapin, BLOS1, BLOS2 and BLOS3 5,6 . Electron microscopy revealed that the subunits of BLOC-1 are arranged in a stable elongated structure of eight globular cores 7 . There is strong evidence that all subunits are required to form a stable complex and lack of one subunit destabilizes the complex and causes a drop in levels of the other subunits, as observed in null mouse models for dysbindin (sandy, sdy), BLOS3 (reduced pigmentation, rp), muted (mu) and pallidin (pa) 6,8,9 .