Designing high density DNA arrays representing all the genes of an organism could be limited when the entire genome sequence of the organism is not available or if only a limited number of ESTs are available. In an effort to prepare coding sequences as DNA sources for a microarray, we found that coding region enriched genomic DNA libraries can be produced by S1 nuclease treatment of partially denatured genomic DNA. Sequence analysis of about 1,000 clones using BLASTN and BLASTX searches showed that 46% of the clones in the library have regions which share significant similarity with sequences deposited in the rice EST and nr data bases. These data suggested that clones produced in this library could be directly used as PCR templates, where the resulting PCR products could be spotted on slides for microarray analysis. This technique might be applicable in designing a high density DNA array for an organism whose entire genome sequence is not available.