The present invention provides, among other things, methods for purifying high quality messenger RNA (mRNA) suitable for clinical use, without using any caustic or flammable solvents. The present invention is, in part, based on surprising discovery that mRNA can be successfully purified by selective precipitation and washing without using ethanol while maintaining integrity and high purity of mRNA. Thus, the present invention provides an effective, reliable, and safer method of purifying RNA from large scale manufacturing process therapeutic applications without using any caustic or inflammable solvents.