The microarray technology allows the high-throughput quantification of the mRNA level of thousands of genes under dozens of conditions, generating a wealth of data which must be analyzed using some form of computational means. A popular framework for such analysis is Matlab, a powerful computing language for which many functions have been written. However, although complex topics like neural networks or principal component analysis are freely available in Matlab, functions to perform more basic tasks like data normalization or hierarchical clustering in an efficient manner are not. The MatArray toolbox aims at filling this gap by offering efficient implementations of the most needed functions for microarray analysis. The functions in the toolbox are command-line only, since it is geared toward seasoned Matlab users.