Gene Expression Pattern Scanner (GEPS) is a web-based server to provide interactive pattern analysis of user-submitted microarray data for facilitating their further interpretation. Putative gene expression patterns such as correlated expression, similar expression and specific expression are determined globally and systematically using geometric comparison and correlation analysis methods. These patterns can be visualized via linear plot with quantitative measures. User-defined threshold value is allowed to customize the format of the pattern search results. For better understanding of gene expression, patterns derived from 329,205 non-redundant gene expression records from the GNF SymAltas and the Gene Expression Omnibus are also provided. These profiles cover 24,277 human genes in 79 tissues, 32,905 mouse genes in 61 tissues and 4201 rat genes in 44 tissues. GEPS is available at http://bioinf.xmu.edu.cn/software/geps/geps.php.