Gene expression is a complex process that establishes and maintains a specific cell state. Transcription, an early event during the gene expression, is fine-tuned by a concerted action of a plethora of transcription factors temporally and spatially in response to various stimuli. Most of the earlier research has focused on the initiation of transcription as a key regulatory step. However, work done over the last two decades has highlighted the importance of regulation of transcription elongation by RNA Pol II in the implementation of gene expression programs during development. Moreover, accumulating evidence has suggested that dysregulation of transcription elongation due to dysfunction of transcription factors can result in developmental abnormalities and a broad range of diseases, including cancers. In this chapter, we review recent advances in our understanding of the dynamics of transcription regulation during the elongation stage, the significance of transcriptional regulatory complexes, and their relevance in the development of potential accurate therapeutic targets for different human diseases.