The analysis of network properties of metabolic systems has recently attracted increasing interest. While enzymes are usually considered to be specific catalysts, many enzymes in living cells are characterized by broad substrate specificity. Here we discuss some aspects of the treatment of such multifunctional enzymes in metabolic pathway analysis, for example, their suitable representation. The fact that the choice of independent functions of multifunctional enzymes is non-unique is explained. We comment on the annotation of such enzymes in metabolic databases and give some suggestions to improve this. We then explain the proper definition of metabolic pathways (elementary flux modes) for systems involving multifunctional enzymes and discuss some ontological problems.