AbstractBackgroundRecent studies have shown that in Arabian horse muscle, long‐term exercise‐induced expression of genes related to fatty acid degradation and the downregulation of genes belonging to the glycolysis/gluconeogenesis and insulin signalling pathways. Long‐lasting physical exertion may trigger the metabolism to switch the main energy source from carbohydrates to lipids due to higher caloric content.ObjectivesTo describe the metabolism adaptation at the whole transcriptome of blood to endurance effort in Arabian horses.Study designIn vivo experiment.MethodsVenous blood samples from 10 Arabian horses were taken before and after a 120 km long endurance ride to isolate the RNA and perform the high‐throughput NGS transcriptome sequencing.ResultsThe results, including KEGG (Kyoto Encyclopaedia of Genes and Genomes) and GO (Gene Ontology) analyses, allowed us to describe the most significantly upregulated—ARV1, DGAT2, LIPE, APOA2, MOGAT1, MOGAT2, GYS1, GYS2 and downregulated—ACACA, ACACB, FADS1, FADS2 genes involved in carbohydrate and lipid metabolism. Also, the increased expression of RAF1, KRAS and NRAS genes involved in the Insulin pathway and PI3K–Akt was shown.Main limitationsLimited sample size, Arabians used for endurance racing were not compared to Arabians from other equestrian disciplines.ConclusionsThis general insight into the processes described supports the thesis of the lipid‐carbohydrates metabolism switch in endurance Arabian horses and provides the basis for further research.