We studied the neural substrates of higher-order conditioned fear in rats. We first studied acquisition and extinction of second-order fear. One stimulus (S1) was paired with a footshock unconditioned stimulus (US), a second stimulus (S2) was paired with S1, and, finally, fear of S2 was extinguished by S2 alone exposures. Reversible inactivation of the basolateral amygdala (BLA) via muscimol, systemic injection of the NMDA receptor (NMDAr) antagonist MK-801 [(+)-5-methyl-10,11-dihydro-5H-dibenzo [a,d] cyclohepten-5,10-imine maleate], or intra-amygdala infusion of the NMDAr NR2B subunit selective antagonist ifenprodil impaired both acquisition and extinction of fear to S2. We then studied acquisition and extinction of sensory preconditioned fear. S2 was first paired with S1, S1 was then paired with the US, and, finally, fear of S2 was extinguished by S2 alone exposures. Extinction of sensory preconditioned fear was impaired by a BLA infusion of muscimol or ifenprodil and by MK-801. Acquisition of the S2-S1 association and extinction of this association by S2 alone exposures before conditioning of S1 was impaired by MK-801 but not by a BLA infusion of muscimol. These results show that NMDAr activation in the BLA is critical for acquisition of second-order conditioned fear and for the extinction of both second-order and sensory preconditioned fear just as it is for acquisition and extinction of first-order conditioned fear. Acquisition and extinction of an association between two neutral stimuli also require NMDAr activation. However, the present results show that the acquisition and extinction of these associations do not require the BLA.