Ultrasound (US) can influence plant growth and development. To better understand the genetic mechanism underlying the physiological response of potato to US, single-node segments of four-week-old in vitro plantlets were subjected to US at 35 kHz for 20 min. Following mRNA purification, 10 cDNA libraries were assessed by RNA-seq and significantly differentially expressed genes (DEGs) were categorized by gene ontology (GO) or Kyoto Encyclopedia of Genes and Genomes (KEGG) identifiers. The expression intensity of 40,430 genes from a total pool of 45,112 genes were studied. From these, several hundred genes associated with biosynthesis, carbohydrate metabolism and catabolism, cellular protein modification, and response to stress, and expressed mainly in the extracellular region, nucleus, and plasma membrane, were either up- or down-regulated in response to US. This study examines how some processes evolved over time (0 h, 24 h, 48 h, 1 week and 4 weeks) after an abiotic stress (US) was imposed on in vitro potato explants, and provides important clues to the temporal dynamics in enzyme and DEG profiles in response to this stress as the explant becomes established in vitro. Despite this abiotic stress, plantlets survived. Overall design: mRNA transcription profile of potato (Solanum tuberosum L.) under US stress conditions.