Maternal anxiety and depression are significant risk factors for the development of these disorders in offspring. The pathways through which risk is conferred remain unclear. This study examined fear acquisition and extinction in 26 children at high risk for emotional disorders by virtue of maternal psychopathology (n = 14 with a mother with a principal anxiety disorder and n = 12 with a mother with a principal unipolar depressive disorder) and 31 low risk controls using a discriminative Pavlovian conditioning procedure. Participants, aged between 7 and 14 years, completed 16 trials of discriminative conditioning of two geometric figures, with (CS+) and without (CS-) an aversive tone (US), followed by 8 extinction trials (4 נCS+, 4 נCS-). In the context of comparable discriminative conditioning, children of anxious mothers showed larger skin conductance responses during extinction to the CS+ compared to the CS-, and to both CSs from the first to the second block of extinction trials, in comparison with low risk controls. Compared to low risk controls, children of depressed mothers showed smaller skin conductance responses to the CS+ than the CS- during acquisition. These findings suggest distinct psychophysiological premorbid risk markers in offspring of anxious and depressed mothers.