Here, we analyze the specificity and reproducibility of nucleic acid hybridization to oligonucleotide microarrays used in the large-scale mutational analysis of the ATM (ataxia telangiectasia mutated) gene that is responsible for autosomal recessive disorder involving cerebellar degeneration, immunodeficiency, radiation sensitivity and cancer predisposition and is also commonly mutated in certain lymphoid malignancies (32, 33) . These microarrays include 25mer oligonucleotide probes complementary to all possible single base substitutions and insertions as well as one and two base deletions on both strands of the ATM coding region. This provides the first comparative analysis of the hybridization properties of substitution, insertion and deletion probes in an oligonucleotide microarray-based mutational analysis of a large gene.