The classic view of metabolism as a collection of metabolic pathways is being questioned with the currently available possibility of studying whole networks. Novel ways of decomposing the network into modules and motifs that could be considered as the building blocks of a network are being suggested. In this work, we introduce a new definition of motif in the context of metabolic networks. Unlike in previous works on (other) biochemical networks, this definition is not based only on topological features. We propose instead to use an alternative definition based on the functional nature of the components that form the motif. After introducing a formal framework motivated by biological considerations, we present complexity results on the problem of searching for all occurrences of a reaction motif in a network, and introduce an algorithm that is fast in practice in most situations. We then show some initial applications to the study of pathway evolution and of the global structure of metabolic networks.