Fragile X syndrome is the most common genetically inherited cause of neurodevelopmental disability in humans, affecting approximately 1:2000 to 4000 live births. Affected individuals have significant, long-term problems with learning, and often with behavior as well. The disorder is caused by the presence of a greatly expanded CGG repeat within the FMR1 gene on the long arm of the X chromosome. Abnormal methylation of this repeat, and adjacent areas within the FMR1 gene impedes transcription, ultimately resulting in reduced production of the FMR1 protein (FMRP). This protein is expressed in neurons, with particularly high levels of gene transcription occurring in the nucleus basalis (basal forebrain) and hippocampus. A recent functional imaging study from our group showed girls with fragile X to have greatly reduced levels of brain activation in the basal forebrain and hippocampal activation during a memory task. The nucleus basalis, is a cholinergic nucleus with widespread connections to the neocortex. It is critical to visuospatial attention in rodents and primates and is presumed to play a similar role in humans. The finding of decreased basal forebrain activation in girls with fragile X, considered in light of histological evidence showing high transcription levels of FMR1 in healthy nucleus basalis, suggests the possibility of a functional cholinergic deficit in fragile X syndrome.