Difficulty down-regulating negative affect has been linked with anxiety and depression. In addition, recent studies have identified specific polymorphisms of the MAOA gene related to affective psychopathology. Here we examined whether genetic variation in MAOA was associated with the time course of responses to affective stimuli. Emotion-modulation of the startle blink response was measured during and after affective pictures. Women with the G/G genotype of the MAOA T941G single nucleotide polymorphism showed sustained reactivity to unpleasant stimuli, as evidenced by continued blink potentiation during the picture-offset period. These data suggest that the MAOA T941G polymorphism, which has been previously linked with mood disorders, is associated with a maladaptive pattern of affective responding in women.