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Pathway analysis can complement point‐wise single nucleotide polymorphism (SNP) analysis in exploring genomewide association study (GWAS) data to identify specific disease‐associated genes that can be candidate causal genes. We propose a straightforward methodology that can be used for conducting a gene‐based pathway analysis using summary GWAS statistics in combination with widely available reference genotype data. We used this method to perform a gene‐based pathway analysis of a type 1 diabetes (T1D) meta‐analysis GWAS (of 7,514 cases and 9,045 controls). An important feature of the conducted analysis is the removal of the major histocompatibility complex gene region, the major genetic risk factor for T1D. Thirty‐one of the 1,583 (2%) tested pathways were identified to be enriched for association with T1D at a 5% false discovery rate. We analyzed these 31 pathways and their genes to …