Objective: To standardize an RNA (ribonucleic acid) extraction protocol in children's saliva specimens. Methods: The study was conducted on saliva specimens from 60 children who participated in the study with their parents' authorization. Comparison of two RNA extraction methods was established; methods assessed concentration, quality and yield. Moreover, genic expression of GUSB gene was achieved with RT-PCR (reverse transcriptasepolymerase chain reaction). Data were analyzed through measurements of central tendency and dispersion, frequencies and percentages. T-Student and χ2 tests were used in order to differentiate between both methods (p < 0.05). Results: Analysis of cell amounts per saliva ml revealed a mean of 564,977.8 (SD = 246,678.6); a RNA in children's saliva extraction method was standardized, specifically the method using RNeasy® Protect Saliva Mini Kit Qiagen exhibited better characteristics of RNA concentration (p = 0.0000) and yield (p = 0.0000) when compared to the method using QIAzol®; no RNA (p = 0.146) quality differences were found. Conclusions: RNA could be extracted from children's saliva specimens, therefore, it is suggested to use saliva for the molecular analysis of different oral and systemic diseases.