Expression of neural differentiation-associated genes was examined by RT-PCR and macroarray analyses during neural differentiation of P19 embryonal carcinoma cells induced by cell aggregation and/or retinoic acid (RA) treatment. Results revealed that the neural genes examined could be classified into 4 groups based on their expression patterns. The 1st group included the Wnt-1, Id-1, Id-3 and cdc42 genes, expression of which was altered by cell aggregation alone, but not by RA treatment alone. The 2nd group included the alphaN-catenin, Neuro D and GDNFRbeta genes, expression of which was altered by RA treatment alone, but not by cell aggregation. The 3rd group consisted of the Brn-2, TrkA, bcl-X, N-cadherin, E-cadherin and Otx-2 genes, expression of which was altered by either treatment. The 4th group included the ACTH, D4DR, NGC and Oct-3 genes, the expression of which changed only when both treatments were applied simultaneously. Expression of the Ets-1 and Fli-1 transcription factor genes was up-regulated by either treatment alone at initial stages of neural differentiation of P19 cells, although overexpression of these genes alone could not induce cell differentiation. Our results suggest that although both treatments are required for complete neural differentiation of P19 cells, cell aggregation or RA treatment alone drive differentiation to a certain extent at the gene expression level.