Boar taint (BT) is an offensive odour or taste of meat from a proportion of non-castrated male pigs due to skatole and androstenone accumulation in adipose tissue. Castration is an effective strategy to avoid BT but is currently under debate due to animal welfare concerns. This study aimed to functionally characterise and evaluate important expression quantitative trait loci (eQTL) to identify potential causal mechanisms of BT for use in optimised breeding for reduced BT without castration. Danish Landrace male pigs (n=48) with low, medium and high genetic merit of BT were slaughtered at 100 kg. Gene expression profiles were obtained by RNA-Seq and genotype data was obtained by Illumina 60K Porcine SNP-chip. Following quality control and filtering, 10,545 and 12,731 genes from liver and testis were included in eQTL analysis by the Matrix eQTL software together with 20,827 SNP variants. A total of 180 eQTLs containing 66 genes and 278 eQTLs containing 117 genes were mapped respectively in liver and testis with a significant (FDR < 0.05) gene-SNP relationship and association (P < 0.05) with BT phenotype. Functional enrichment test of eQTLs revealed biological processes within negative regulation of DNA replication, cell activation and DNA metabolic processes. By employing a multivariate Bayesian Hierarchical Model within Matrix eQTL, a total of 26 eQTLs containing 12 genes were mapped as multi-tissue eQTLs (FDR < 0.05) and having significant association (P < 0.05) to the BT phenotype. Enrichment test of multi-tissue eQTLs with known QTLs revealed 46 QTLs to have significant (P < 0.05) overlap which were mainly traits categorised as meat and carcass QTLs, meat and carcass associations and production QTLs. The overlap of the QTL and eQTLs show potential causality for BT phenotypes. Finally, the unique 12 genes from the multi-tissue eQTLs were evaluated with respect to their role in BT and possible role as candidate biomarkers of BT in optimised breeding scenarios.