Profound, long-term behavioral and physiological consequences have been identified with, and attributed to prior exposure to severe early life stressors vis-à-vis altered maternal responses. To date, questions remain unanswered regarding potential changes of both functional brain activity and molecular expression of progeny that corresponds with known behavioral and physiological alterations in adulthood. Furthermore, questions regarding potential molecular changes during gestation, particularly related to neuro-development have remained elusive. For instance, given the potency of stress hormones, do foetuses, when exposed to excess quantities, have an aberrant rate in programmed cell death, or alterations of epigenetic markers to an important gene related to proper brain and neuron formation? Here, for the first time, we show localization of functional brain activity and it’s corresponding molecular profile, programmed cell death, during the conditioned fear paradigm of adult animals with and without prior history of antenatal maternal stress. Also, we offer preliminary data that indicates the epigenetic profile of neuronatin, a critical gene for proper brain and neuron development, was changed from chronic exposure to gestational stress.