The latest trends in the paper industry have been towards manufacturing by a neutral or alkaline process, greater consumption of secondary fibres and the closing-up of the process water systems. Under these conditions of papermaking, the problems of deposits, corrosion and odours due to the microbiological activity increase considerably and therefore, runnability and production problems occur. To help our understanding of the current situation in the paper industry, this paper presents a review of the microorganism sources, the consequences of the microbiological activity upon the actual systems of manufacturing paper and board; and the current state of the different alternatives for its prevention and control, as well as the future trends to address environmental considerations.