Genetic factors that modulate the immune response have been implicated as risk factors for schizophrenia and cognitive impairment. We assessed the correlation between cognitive functioning and the LTA Cys13Arg polymorphism in 351 individuals with schizophrenia, 122 with bipolar disorder, and 160 controls. There was a significant association between cognitive functioning and the LTA Cys13Arg polymorphism within the schizophrenia (p <0.008) but not the other diagnostic groups. There was no association between cognitive functioning and the two other polymorphisms in the same gene complex. The LTA Cys13Arg polymorphism may represent a risk factor for cognitive impairment in individuals with schizophrenia.