Purpose. Ocular growth is regulated locally by signals produced in the retina. The highly heterogeneous nature of the retina may mask important changes in gene expression during global analysis. This study was conducted to investigate changes in gene expression specifically within the amacrine cell layer (ACL), the most likely generator of growth signals, during optical manipulation of ocular growth. Method. Chicks were monocularly treated with either - 7-D (n = 6) or +7-D (n = 6) lenses for 24 hours. Untreated age-matched chicks served as control subjects (n = 6). Total RNA from the ACL was isolated from 10-fxm-thick sections, obtained using laser capture microdissection. Labeled cRNA was prepared from three samples per condition and hybridized to chicken genome microarrays. Changes in gene expression were validated by using semiquantitative real-time RT-PCR. Results. One hundred twenty-eight genes were differentially expressed in the ACL of the minus lens-treated eyes, whereas the plus lens-treated eyes displayed 58 changes 24 hours after treatment. Only 11 genes were differentially expressed under both experimental conditions, whereas the expression of only one gene (clone ChEST927g14) was modulated by the sign of defocus. Compared with previous studies in the field, the magnitude of changes observed in the present work were larger, with more than 30% of differentially expressed genes showing a twofold or greater modulation in expression. The results, obtained from independent validation by real-time RT-PCR technology, correlated highly with the original microarray data. The differential expression of four of eight genes was validated in plus lens-treated eyes, and eight of nine genes were independently validated in minus lens-treated eyes.Conclusions. The targeted investigation of the ACL enabled the identification of several novel genes that may form part of the growth regulatory pathways of the eye. Different retinal pathways may underlie the response of the eyes to plus and minus lens compensation, as there was limited overlap in the regulated genes observed within the ACL under both conditions.