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In the search for optimal platforms for protein expression and secretion, filamentous fungi in principle provide some of the best microbial cell factories. They are inherently endowed with the ability to secrete proteins. Fungi belonging to Aspergillus and Trichoderma species are well-studied for industrial production of proteins and enzymes. Our understanding of these organisms at the level of transcription, translation, post-translational processing and the secretory pathways has improved significantly in recent years. Despite this, the ability of these fungal secretion platforms has not yet been able to match their intrinsic secretion capacity to produce foreign proteins. Details of the molecular mechanisms of the secretory pathways in filamentous fungi are emerging. This knowledge can be gainfully employed to enhance protein production in filamentous fungi, particularly in the secretion of heterologous proteins of value.