Gonadal steroid hormones play an important role in the process of sexual differentiation of brain areas and behavior such as singing and song learning in songbirds. These hormones affect behavior controlling circuits on both the gross morphological and ultrastructural levels. Here we study whether the expression of genes coding for synaptic proteins is sensitive to gonadal steroid hormones and whether such altered expression coincides with changes in brain area size. We treated adult male zebra finches with the aromatase inhibitor fadrozole, to reduce estrogen synthesis and analyzed the mRNA expression of the synaptic proteins synaptoporin (SPO) and synaptosomal-associated protein 25 kDa (SNAP-25) in song control areas and surrounding tissues of adult male zebra finches. SPO and SNAP-25 are differently expressed throughout the song system. Generally, the telencephalic song nuclei expressed SNAP-25 at high intensity whereas SPO expression was area-specific. Elevated levels of SNAP-25 mRNA were present in the nucleus hyperstriatalis ventrale pars caudale (HVC) and in the robust nucleus of the archistriatum (RA). SPO mRNA was found in moderate levels in the HVC, in low levels in the lateral nucleus magnocellularis (lMAN) and Area X, and was absent in the RA. The treatment significantly increased the mRNA level of SPO in the HVC, whereas SNAP-25 expression level was not affected. These expression patterns are not explained by the decrease of HVC volume after treatment. The decreased HVC size is not area-specific but correlates with an overall reduction in size and an overall increase in cell density of the forebrain. © 2004 Wiley-Liss, Inc.