We have developed a new strategy for differential screening of genes that are expressed in two or more tissues, and have used it to identify genes that are preferentially expressed in both testis and ovary. In this approach, testis-specific cDNAs were first generated using the suppression subtractive hybridization technique, cloned and arrayed in microplates. The inserts from the subtracted testis-specific library were amplified by PCR and spotted on filters. The dot blots were screened by hybridization using either testis- or ovary-specific subtracted cDNA mixtures as probes. By screening about 2000 putative clones from the subtracted testis-specific library, we identified 14 candidate genes that hybridized to both cDNA probes. Northern blot analysis showed that 12 clones were preferentially or exclusively expressed in testis and ovary. Nucleotide sequence analysis indicated that three of the identified clones represented cDNAs from novel genes.