Boar taint (BT) is an offensive odour or taste of porcine meat which may occur in entire male pigs due to skatole and androstenone accumulation. To avoid BT, castration of young piglets is performed but this strategy is under debate due to animal welfare concerns. The study aimed to reveal potential BT biomarkers for optimized breeding. Male pigs (n=48) with low, medium and high genetic merit of BT were selected and tissues from liver and testis were subjected to transcriptomic profiling by RNA-Seq. The reads were mapped to the Sus scrofa reference genome (Ensembl, ver. 79) which resulted in ~87% uniquely mapped reads. Quality control by Qualimap revealed ~51% of reads mapped in the exonic. Differential expression (DE) comparison of low, medium and high BT using Limma revealed a 10-fold difference in numbers of DE genes (FDR < 0.05) between liver and testis, with testis being the highly active tissue. GOseq was used to find enriched gene ontology (GO) terms and REVIGO was used to filter semantic similarities. In both liver and testis, a GO termed “oxidoreductase activity” was enriched (p < 0.05) due to high amounts of 5α-reductases involved in steroid metabolism, including androstenone synthesis. In testis, >80 DE genes were functionally classified by the PANTHER tool to “Gonadotropin releasing hormone receptor” and “Wnt signaling” pathways which play a role in reproductive maturation and proliferation of spermatogonia, respectively. WGCNA was used to build co-expression modules and enrichment analysis and semantic filtering revealed the GO terms “catalytic activity” and “transferase activity” to be overrepresented (p < 0.05) in liver and testis, respectively. Transferases include prenyltransferases which are involved in catalysis of the precursor of steroid hormones. Extraction of hub genes from important modules and integration with DE results revealed potential biomarkers for BT.