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Introduction Malignant hyperthermia (MH) is a rare autosomal dominant pharmacogenetic disorder which known associated with some genes such as CACNA1S and RYR1. Using whole exome analysis, we aimed to find out the genetic variant data in a malignant hyperthermia patient undergoing cardiac surgery. Presentation of case Patient was 59 years old male with dull left chest pain, mild breathing difficulty, thrombosis in the left atrium, mitral valve stenosis that needed a surgery to remove the thrombus and replace the mitral valve. After 5-h operation of left mitral heart valve replacement using both intravenous and inhaled anaesthetics, the patient showed suddenly hyperthermia (39.5 °C), low blood pressure (90/50 mmHg), heavy sweating, 1 mm dilated pupils on both sides, positive light reflection. Whole exome analysis showed 96,286 of SNPs including 11,705 of synonymous variants, 11,388 of missense variants, 106 of stop gained, and 39 of stop lost. One variant of RYR1 gene was found as mutation point at c.7048G > A (p.Ala2350Thr) known related to MH. Discussion This was a rare case of MH during cardiac surgery reported in Vietnam that might related to mutation point at c.7048G > A (p.Ala2350Thr) of RYR1 gene. Conclusion Patient carried a mutant of RYR1 gene could possibly lead to MH development post anaesthesia of cardiac surgery., Highlights • A male cardiac surgery patient got malignant hyperthermia post anaesthesia. • Whole exome variant analysis showed a mutant variant in RYR1 gene of patient. • RYR1 gene testing might need to avoid MH during surgery using inhaled anaesthetics.