Reconstructive surgery of the peripheral nerve has undergone major technical improvements over the last decades, leading to a significant improvement in the clinical outcome of surgery. Nonetheless, functional recovery remains suboptimal in the majority of patients after nerve repair surgery. In this review, we first discuss the molecular mechanisms involved in peripheral nerve injury and regeneration, with a special emphasis on the role of neurotrophic factors. We then identify five major challenges that currently exist in the clinical practice of nerve repair and their molecular basis. The first challenge is the slow rate of axonal outgrowth after peripheral nerve repair. The second problem is that of scar formation at the site of nerve injury, which is detrimental to functional recovery. As a third issue, we discuss the difficulty in assessing the degree of injury in closed traction lesions without total loss of continuity of the involved nerve elements. The fourth challenge is the problem of misrouting of regenerating axons. As a fifth and final issue we discuss the potential drawbacks of using sensory nerve grafts to support the regeneration of motoneurons. For all these challenges, solutions are likely to emerge from (a) a better understanding of their molecular basis and (b) the ability to influence these processes at a molecular level, possibly with the aid of viral vectors. We discuss how lentiviral vectors have been applied in the peripheral nerve to express neurotrophic factors and summarize both the advantages and drawbacks of this approach. Finally, we discuss how lentiviral vectors can be used to provide new, molecular neurobiology-based, approaches to address the clinical challenges described above.