With the invention of high throughput methods, researchers are capable of producing large amounts of biological data. During the analysis of such data the need for a functional grouping of genes arises. In this paper, we propose a new method based on spectral clustering for the partitioning of genes according to their biological function. The functional information is based on Gene Ontology annotation, a mechanism to capture functional knowledge in a shareable and computer processable form. Our functional cluster method promises to automates, speed up and therefore improve biological data analysis.