Salivary gland cancers comprise a heterogeneous group of neoplasms whose biological and clinical characteristics differ considerably from those of mucosal squamous cell carcinomas of the head and neck. One of the most common subtypes, adenoid cystic carcinoma (ACC), is notable for its myoepithelial differentiation, proclivity for hematogenous spread, and slow but progressive clinical course. The molecular alterations that underlie its development and progression are poorly characterized. Here we used oligonucleotide microarray analysis to survey the expression of 8920 different human genes in 15 ACCs, one ACC cell line, and five normal major salivary glands. We observed expression of genes indicative of myoepithelial differentiation, as expected, including those whose protein products are components of basement membranes and extracellular matrix. Other genes that were highly ranked for their expression in ACC were those encoding the transcription factors SOX4 and AP-2␥, the latter of which also was overexpressed in ACC relative to 175 other carcinomas from 10 anatomical sites that we had previously profiled. Additional genes, which were highly expressed in ACC compared to the other carcinomas, included casein kinase 1, epsilon and frizzled-7, both members of the Wnt/-catenin signaling pathway. Our study documents for the first time the diverse spectrum of genes overexpressed in ACC and highlights gene products and pathways that in the future might be exploited as therapeutic targets for this cancer, which up until Unlike mucosal squamous cell carcinomas of the head and neck, carcinomas of the salivary glands consist of a diverse histopathological spectrum of neoplasms. Adenoid cystic carcinoma (ACC) is one of the most common subtypes of salivary gland cancer, and in several series is the most frequent malignant tumor of the submandibular and minor salivary glands. 1,2 Histopathologically, ACC often forms both true lumens as well as pseudolumens in varying proportions. It characteristically shows myoepithelial differentiation and produces in large amounts specific proteins that comprise basement membranes and extracellular matrix. 3 The neoplasm has a proclivity for invading nerves, but it infrequently spreads via the lymphatic system. ACC has a protracted clinical course with local recurrences, hematogenous metastases, and poor response to classical chemotherapeutic approaches. After surgery and radiation therapy for patients with ACC, the disease-specific survival at 15 years is ϳ40%. 4 The constellation of genes that are critical for the development and progression of ACC are not known. Furthermore, genes whose expression in ACC is altered relative to those in normal salivary glands and other carcinomas have not yet been compiled. In this study, we used large-scale microarray analysis in an effort to characterize the expression profiles in this salivary gland malignancy, and to specifically identify those genes differentially expressed between ACC and normal salivary gland epithelium. Importantly, we have als...