Deprivation of auditory nerve input in young mice results in dramatic neuron death in the anteroventral cochlear nucleus (CN), while the same manipulation performed in older mice does not result in significant neuronal loss. The molecular basis underlying this critical period of susceptibility to loss of afferent input remains largely unknown. One possibility is that developmental differences in baseline mRNA expression of specific genes could predispose CN neurons to either death or survival after deafferentation. We used two microarray platforms to identify differentially expressed genes in the CN during and after this critical period. Results across platforms were also compared to each other. Three ages were examined; during the critical period (postnatal day (P)7), at the closing of the critical period (P14), and 1 week after the critical period (P21). Of all the genes surveyed (22,690 or 15,247), 1,082 were identified as significantly changed in expression during the critical period relative to after. Real-time reverse transcription polymerase chain reaction and immunohistochemistry confirmed and extended the microarray results for a subset of these genes. Further analysis of genes related to apoptotic pathways showed 6 out of 7 differentially expressed known pro-apoptotic genes had higher expression during the critical period. In contrast, 9 out of 11 differentially expressed known pro-survival genes increased after the critical period when CN neurons survive deprivation. This finding supports the concept that multiple neuroprotective mechanisms increase and pro-apoptotic factors decrease over development to protect mature neurons from stressful insults, making them less dependent on afferent input for survival.