Synthetic glucocorticoids (GC) are widely used drugs, also in the prevention of diseases that occur in the preterm newborn. Previously we have found that GC treatment of pregnant rats resulted in a persistent increase in the ratio of AVP over CRH in the mediobasal hypothalamus, and in an increased CD4/CD8 ratio in the thymus of the newborn. The objective of the present study was to investigate whether such effects were also seen after neonatal GC exposure, given in clinically-relevant doses. Dexamethasone-21-phosphate (DEX; 1.2 microg/g BW, i.p.) was given at day 5 and day 7 after birth. At day 18, 33, and 48 after birth effects of GC on the HPA-axis, and on CD4+ and CD8+ T cells in thymus and spleen were examined. Neonatal DEX treatment temporarily increased (p < 0.01) AVP stores in the external zone of the median eminence (ZEME) on day 18 after birth, and did not affect CRH stores. Resting plasma levels of ACTH and corticosterone remained unchanged after neonatal DEX treatment at any time interval studied. In the thymus and spleen, neonatal DEX treatment decreased (p < 0.0001) T cell numbers on day 18 after birth. Furthermore, neonatal DEX treatment increased (p < 0.01) the ratio of mature CD4-CD8+ over CD4-CD8+ thymocytes on day 18 after birth, but not on day 33 and day 48 after birth. In conclusion, neonatal DEX treatment has temporary effects on peptide expression in hypothalamic CRH neurons, and on thymocyte maturation. Apparently, neonatal exposure to GC affects potentially sensitive targets within the endocrine system and immune system but these alterations are reversible and readjusted during development.