Microarray experiments are widely used in biological research, permitting the concurrent monitoring of gene expressions levels on the genome scale. In an optimal microarray experiment surface-bound (probe) DNA hybridizes exclusively with its specific target - typically fluorescent cDNA synthesized from mRNA. However, unintentional yet specific interactions do occur (cross-hybridization) due to regions of complementary sequence among probes and targets, affecting the reliability of microarray experiments. We have developed a program that simulates the hybridization processes in microarray experiments, explicitly accounting for the effects of hybridization. The program can be used to evaluate the performance and robustness of proposed microarray probe sequence designs and assist in the evaluation and interpretation of the results of microarray experiments.