Salivary biomarkers for diagnostic and prognostic assessments have become increasingly well established in recent years. Salivary mRNA transcriptomic analyses create a new paradigm in the emerging field for noninvasive molecular diagnosis. In this chapter, we will overview the development of sensitive and robust microarray and multiplex quantitative reverse transcriptase-PCR assays for the discovery and validation of mRNA biomarkers in human saliva. Total RNA isolated from human saliva is used for microarray profiling through Human Genome U133 Plus 2.0 and Exon 1.0 ST array platforms. A universal RNA linear amplification strategy was used to amplify RNA from nanogram scale followed by reverse transcription-PCR reaction, cleaned up enzymatically, and validated by quantitative PCR. Further, the integrity of RNA can be analyzed by the Agilent Bioanalyzer and quantified using a Nanodrop microvolume spectrophotometer. Using these invaluable technical tools, one can identify thousands of mRNA species in saliva. These methods indicate that salivary mRNA provides an efficient medium for biomarker discovery in oral and systemic diseases detection.