The need to sleep is universal and lack of sleep often results in decreases in alertness and cognitive function. Data suggest that sleep-related mechanisms and deficits resulting from loss of sleep are associated anatomically with the basal forebrain. Long-term effects of sleep deprivation, those lasting a day or more, likely require transcriptional changes leading to changes in protein synthesis, whereas short-term effects may be mediated by rapid changes in the functional status of proteins. To understand sleep deprivation-induced changes in proteins in the wake-promoting area of the basal forebrain in rat, proteomic analysis was carried out by a combination of 2D gel electrophoresis to separate and visualize proteins and matrix-assisted laser desorption/ionization time-of flight mass spectrometry for protein identification. Among 969 protein spots that were compared, 89 spots showed more than a twofold difference between 6-hr sleep-deprived rats and undisturbed sleeping controls. We have identified 11 of these proteins to be either cytoskeletal or associated with synapses. The changes in four of these proteins were analyzed further by Western blots of 1D and 2D. Two proteins associated with the cytoskeleton, tubulin and GAP43, show posttranslational modifications. Increased tyrosination of alpha tubulin isoforms and increased phosphorylation of GAP43 was observed after 6-hr sleep deprivation when compared to that in sleeping controls. The synaptic protein synaptosomal-associated protein-25 (SNAP25) is decreased whereas amphiphysin is phosphorylated after sleep deprivation. These changes in proteins in the basal forebrain during short-term sleep deprivation are suggestive of changes in the substrate for neuronal transmission and plasticity.