MOTIVATION: The development of the omics technologies such as transcriptomics, proteomics and metabolomics has made possible the realization of systems biology studies where biological systems are interrogated at different levels of biochemical activity (gene expression, protein activity and/or metabolite concentration). An effective approach to the analysis of these complex datasets is the joined visualization of the disparate biomolecular data on the framework of known biological pathways. RESULTS: We have developed the Paintomics web server as an easy-to-use bioinformatics resource that facilitates the integrated visual analysis of experiments where transcriptomics and metabolomics data have been measured on different conditions for the same samples. Basically, Paintomics takes complete transcriptomics and metabolomics datasets, together with lists of significant gene or metabolite changes, and paints this information on KEGG pathway maps. AVAILABILITY: Paintomics is freely available at http://www.paintomics.org.