Phenylketonuria is the most common, inherited aminoacidopathy associated with brain injury. To date, no study has focused on the neuropathology of the genetic mouse model of phenylketonuria, BTBR-Pah(enu2). We examined dendritic spines and synapses in the CA1 and prefrontal cortex among the wild-type, heterozygous, and BTBR-Pah(enu2) mice. A reduced density of dendritic spines, a shortened length of the presynaptic active zone, a widened synaptic cleft, and decreased thickness of postsynaptic density were revealed in BTBR-Pah(enu2) mice. Meanwhile, the phosphorylation at Thr286 of Ca(2+)/calmodulin-dependent protein kinase IIα was alerted in BTBR-Pah(enu2) mice. These findings revealed that phenylketonuria-related brain impairment is accompanied with abnormalities of dendritic spines and synapses. The dysfunction of Ca(2+)/calmodulin-dependent protein kinase IIα may result in an impaired synaptic function.