In spite of numerous publications on potential diagnostic application of circulating DNA and transrenal nucleic acid (Tr‐NA) analysis, few, if any, tests based on this technology are available in clinical labs. This delay in test development and implementation is caused, at least in part, by the deficit in robust methods for isolation of short nucleic acid fragments from bodily fluids, as well as in techniques for analyzing these fragments. We have developed a new anion exchanger‐based method for the isolation of cell‐free nucleic acid fragments from large volumes of bodily fluids, and analyzed these fragments by PCR techniques specially designed to amplify “ultrashort” templates. The combination of these two techniques not only revealed the presence in urine of 10–150 bases or bp DNA and RNA fragments in addition to previously observed 150–200‐bp DNA fragments and high molecular weight DNA, but also significantly increased the sensitivity of Tr‐DNA detection. Additionally, we detected in urine a variety of miRNAs, including those excreted transrenally, thereby opening new diagnostic possibilities for Tr‐NA analysis.