The current biopharmaceutical market is driven by the steady increase in demand for recombinant therapeutics produced in mammalian cell lines. Chinese hamster ovary (CHO) cells are the predominant workhorses for large-scale stable expression of human glycoproteins. However, the low throughput and time-consuming process of cell line development, heterogeneity and instability of CHO cell lines pose serious challenges. This review highlights the conventional expression system with its limitations and the recent advances in high throughput screening methods for rapid clonal selection, targeted gene integration methods for precise prediction of transcriptional activities, and engineering of DNA elements to improve the stability of CHO cell lines.