The setup of flow cell systems for the study of microbial biofilms and methods for the analysis of structural biofilm development are described in this unit. Use of flow cells allows direct microscopic investigation of biofilm development. The biofilms in flow cells develop under hydrodynamic conditions, and the environment can be carefully controlled and easily changed. The protocols in this unit include construction of the flow cell and the bubble trap, assembly and sterilization of the flow cell system, inoculation of the flow cells, running of the system, image capture and analysis, and disassembly and cleaning of the system. In addition, embedding and fluorescent in situ hybridization of flow cell-grown biofilms are addressed.