Genome-wide association study (GWAS) is a new strategy to identify genes and chromosome regions associated with complex traits. A total of 728 Beijing-You chickens from 50 families were genotyped by 60K SNP Illumina iSelect chicken array. GWAS was performed to study the candidate loci affecting thymus weight and spleen weight at 100 days of age. It was found that 24 SNPs were significantly associated with target traits at Bonferroni corrected 5% genome-wise threshold, including Janus kinase 1(JAK1), zinc finger DHHC-type containing 8 (ZDHHC8)、 vav 3 guanine nucleotide exchange factor (VAV3), SATB homeobox 1 (SATB1) and other genes near these SNPs，and 84 SNPs reached both the significance of ‘suggestive linkage’ and 5% chromosome-wise threshold. These identified genes and SNPs offered essential information for understanding of the molecular mechanisms of immune organs development and facilitated the application of marker-assisted selection in diseases-resistance breeding program in chicken.