Individuals with schizophrenia have difficulties in emotional information processing. A relationship between behavioral variables of emotional processing and structural amygdala alterations in schizophrenia has been proposed but not shown, yet. Morphological studies of amygdala size in schizophrenia have yielded inconsistent results. The current study assessed paired associates learning of emotional and neutral faces in 16 subjects with schizophrenia during acute episode and in relative remission after 3 months. Sixteen matched controls were studied for comparison. Subjects also underwent structural magnetic resonance imaging (3D-MRI) at the first time of assessment. Subjects with schizophrenia showed a significant decrease (by 13%) in total size of the amygdala compared to controls, which was more pronounced on the right side. Subjects with schizophrenia improved associative learning of facial identities but not of emotional facial expressions after relative remission of psychotic symptoms. Volume of the right amygdala in subjects with schizophrenia and in controls was significantly related to emotional learning, indicating better learning in subjects with larger amygdala size. Our results indicate that subjects with schizophrenia have a deficit to form associations when emotionally loaded material is used. This deficit seems to be trait-like and independent of disease state. It seems to be linked to size reduction of the right amygdala in schizophrenia.