Severity of maternal childhood maltreatment has been associated with lower infant grey matter volume and amygdala volume during the first two years of life. A developing literature argues that effects of threat (abuse) and of deprivation (neglect) should be assessed separately because these distinct aspects of adversity may have different impacts on developmental outcomes. However, distinct effects of threat versus deprivation have not been assessed in relation to intergenerational effects of child maltreatment. The objective of this study was to separately assess the links of maternal childhood abuse and neglect with infant grey matter volume (GMV), white matter volume (WMV), amygdala and hippocampal volume. Participants included 57 mother-infant dyads. Mothers were assessed for childhood abuse and neglect using the Adverse Childhood Experiences (ACE) questionnaire in a sample enriched for childhood maltreatment. Between 4 and 24 months (M age = 12.28 months, SD = 5.99), under natural sleep, infants completed an MRI using a 3.0 T Siemens scanner. GMV, WMV, amygdala and hippocampal volumes were extracted via automated segmentation. Maternal history of neglect, but not abuse, was associated with lower infant GMV. Maternal history of abuse, but not neglect, interacted with age such that abuse was associated with smaller infant amygdala volume at older ages. Results are consistent with a threat versus deprivation framework, in which threat impacts limbic regions central to the stress response, whereas deprivation impacts areas more central to cognitive function. Further studies are needed to identify mechanisms contributing to these differential intergenerational associations of threat versus deprivation.