Meta-analysis is a valuable tool for the synthesis of evidence across a wide range study types including high-throughput experiments such as genome-wide association studies (GWAS) and gene expression studies. There are situations though, in which we have multiple outcomes or multiple treatments, in which the multivariate meta-analysis framework which performs a joint modeling of the different quantities of interest may offer important advantages, such as increasing statistical power and allowing performing global tests. Here we apply for the first time these methods to data regarding inflammatory bowel disease (IBD), with its two main forms, Crohn’s disease (CD) and Ulcerative colitis (UC), sharing similar symptoms, but differing in the location and extent of inflammation and in complications.The meta-analysis was performed on 4 datasets containing data for 25,409 unique genes/loci from 251 CD patients, 175 UC patients and 159 healthy individuals. We identified 249 statistically significant differentially expressed genes (DEGs) in CD and 38 in UC at an FDR of 1%. 20 of the DEGs were found be common in both disorders. With the use of the global test derived by the multivariate method we also identified 260 statistically significant DEGs, 53 of which were not found in any of the disorders. Pathway analysis revealed important molecular pathways implicated in the pathogenesis of IBD, such as the JAK/STAT and Interferon-gamma signaling pathways, genes involved in carcinogenesis and others. The multivariate method will be useful in future applications.