Abstract Summary: Network motifs in integrated molecular networks represent functional relationships between distinct data types. They aggregate to form dense topological structures corresponding to functional modules which cannot be detected by traditional graph clustering algorithms. We developed CyClus3D, a Cytoscape plugin for clustering composite three-node network motifs using a 3D spectral clustering algorithm. Availability: Via the Cytoscape plugin manager or http://bioinformatics.psb.ugent.be/software/details/CyClus3D. Contact: [email protected] Supplementary Information: Supplementary data are available at Bioinformatics online.