Abstract Summary: We present an interactive web tool for preprocessing microarray gene expression data. It analyses the data, suggests the most appropriate transformations and proceeds with them after user agreement. The normal preprocessing steps include scale transformations, management of missing values, replicate handling, flat pattern filtering and pattern standardization and they are required before performing any pattern analysis. The processed data set can be sent to other pattern analysis tools. Availability: The web interface is accessible through http://bioinfo.cnio.es/cgi-bin/tools/dnarray/preprocess Contact: jdopazo@cnio.es * To whom correspondence should be addressed.