Exposure to theophylline, a phosphodiesterase (PDE) inhibitor, increases the basophilic basal part and conspicuous nucleoli in salivary acini. These histological findings imply increased gene expression. The purpose of this study was to examine the effect of theophylline on the expression of representative genes in the salivary glands which are regulated by cyclic AMP. Male F344 rats received saline or theophylline (50 mg/kg) intraperitoneally. Parotid and submaxillary glands were isolated from rats at 4, 8, and 24 h post-administration, and gene expression for the principal secretory proteins, amylase 1 (AMY1) and cystatin S (CysS), dominant PDE subfamilies 3A and 4D, and a water channel, aquaporin 5 (AQP5) were quantified by RT-PCR. The cyclic AMP concentration was determined by enzyme-immunoassay. Theophylline exposure resulted in a transient increase in mRNA expression for AMY1 in the parotid gland, CysS in the submaxillary gland, and PDE3A in both salivary glands. The cyclic AMP concentration was elevated in both glands. PDE4D and AQP5 gene expressions were not altered in either gland. Our results suggest that theophylline induces cyclic AMP signals through PDE inhibition, leading to enhanced gene transcription and subsequent histological changes.