Consistent annotation of studies using microarrays is critical to optimal management and use of microarray data. Ontologies provide defined and structured terminology suited for this purpose. The Gene Ontology (GO) has aided the analysis of expression studies greatly by providing consistent functional annotation of array sequence features. The intent of the MGED Ontology (MO) is to provide consistent experimental annotation. The MO has been developed as a community effort in support of the Minimum Information About a Microarray Experiment standard and is tied to the Microarray Gene Expression object model. The MO is freely available and has been incorporated into the annotation systems of several public microarray database systems.