Reliable microarray experiments are extremely computationally demanding given the need to perform complex calculations over a multitude of data. Grid computing can provide a remedy to this problem through accelerating the computations associated with microarray normalization, while at the same time providing access to vast amounts of federated storage resources. The present paper presents the application architecture for the HECTOR project, which aims at deploying software for microarray experiments over the Hellenic Grid infrastructure. Emphasis is given on a set of structuring principles that instruct how the various microarray software components are distributed on the Grid. These structuring principles are illustrated in the form of a coherent architecture enabling the operation of microarray applications over the Grid. The description of this architecture is oriented to Grid developers and users, since it focuses on the customization and use of the microarray applications over the Grid, rather than on issues relating to the Grid infrastructure and middleware.