The advent of high throughput technologies and their development in the last two decades have raised great expectations in our capability to solve complex biological and medical problems. This initial hype did not produce the expected results, at least in terms of practical and commercial applications. In particular, gene therapy and tissue engineering initiatives generated a great deal of frustrations and business drawbacks. One possible explanation is the way we still conduct R&D in the field, with every discipline taking care of itself with little or no data analysis integration and almost no multidisciplinary long term projects. Besides, there is still too much empiricism in the way genetic and cellular improvements are sometimes pursued. The concept of integrative genomic engineering offers an opportunity to put together heterogeneous information in a systematic way thus providing an engineering platform for process and product development. We will discuss the pros and cons of the concept and its natural limitations and challenges.