Critically ill preterm infants experience multiple stressors while hospitalized. Morphine is commonly prescribed to ameliorate their pain and stress. We hypothesized that neonatal stress will have a dose-dependent effect on hippocampal gene expression, and these effects will be altered by morphine treatment. Male C57BL/6 mice were exposed to five treatment conditions between postnatal d 5 and 9: 1) control, 2) mild stress + saline, 3) mild stress + morphine, 4) severe stress + saline, and 5) severe stress + morphine. Hippocampal RNA was extracted and analyzed using Affymetrix Mouse Gene 1.0 ST Arrays. Single gene analysis and gene set analysis were used to compare groups with validation by qPCR. Stress resulted in enrichment of gene sets related to fear response, oxygen carrying capacity, and NMDA receptor synthesis. Morphine down-regulated gene sets related to immune function. Stress + morphine resulted in enrichment of mitochondrial electron transport gene sets and down-regulation of gene sets related to brain development and growth. We conclude that neonatal stress alone influences hippocampal gene expression, and morphine alters a subset of stress-related changes in gene expression and influences other gene sets. Stress + morphine show interaction effects not present with either stimulus alone. These changes may alter neurodevelopment.