Ultraconserved regions (UCRs) are 481 DNA segments longer than 200 bp in length that are completely conserved among human, mouse, and rat and, extremely conserved across disparate taxa. More than 90% of UCRs are transcribed (T-UCRs) in normal tissues, but most of them remain uncharacterized. In addition, it was demonstrated that T-UCRs have a tissue-specific expression, and a differential expression profile between tumors and other diseases, which suggests that most of T-UCRs may have an important role in cell processes. However, there is little information about T-UCR characterization or about their molecular mechanisms of action. Taking this into account, in this study, we aim to summarize deregulated T-UCRs in human diseases, emphasizing the ones with stronger functional evidences that are associated with important cell pathways and have a detailed molecular characterization. This article is characterized under: RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.