Numerous eukaryotic expression systems have been developed for use in filamentous fungi since these microorganisms have a high capacity for protein production and secretion. Although commercial exploitation is still at an early stage, a greater understanding of post-translational protein modification and protein secretion mechanisms might help optimize large scale heterologous protein production systems. This is of particular relevance to those proteins that cannot be produced in sufficient quantities in other expression systems. Here, recently developed systems for synthesizing foreign polypeptides in filamentous fungi are reviewed, paying particular attention to the molecular aspects of regulating heterologous gene expression in different hosts. We also evaluate the application of such technology to pathway engineering and protein over-production.