C-terminal binding protein 1 divergent transcript (CTBP1-DT) is a novel long non-coding RNA (lncRNA) located on human chromosome 4p16.3. Numerous studies have shown that CTBP1-DT plays a critical regulatory role in various human malignancies and non-malignant diseases. In several cancers, the expression of CTBP1-DT is upregulated, closely associated with the risk of 12 types of cancer, and strongly correlated with the clinical pathological features and poor prognosis of 10 of these cancers. Mechanistically, CTBP1-DT is stimulated by the transcription factors ETV5 and Sp1, or methylated by YTHDC1. By competitively inhibiting 12 microRNAs, it activates 3 signaling pathways that influence malignant behaviors of tumor cells, including proliferation, apoptosis, cell cycle arrest, migration, invasion, immune evasion, and chemoresistance. Importantly, it also encodes the microprotein DNA damage up-regulated protein (DDUP), which mediates cisplatin resistance through sustained response to DNA damage signals. Furthermore, CTBP1-DT has been implicated in the progression of non-malignant diseases such as diabetes and related conditions, cardiovascular diseases, and osteoarthritis. This review summarizes the latest research on the RNA and protein functions of CTBP1-DT in human diseases, outlines various molecular regulatory networks centered around CTBP1-DT, and discusses the opportunities and challenges of its clinical applications.