Background Congenital cyanotic heart disease (CCHD), inclusive of all types of cyanotic heart disease with resulting hypoxemia and hypoxia, has diverse multisystem effects, including erythrocytosis, hyperviscosity, cholelithiasis, cerebral abscess, vascular dysfunction, and hemoptysis. Most, but not all, patients with CCHD, undergo surgical repair in childhood, resulting in either an elimination or reduction in the degree of hypoxemia and its complications. Systemic-to-pulmonary artery shunt is a necessity as a life-saving procedure that is carried out through placement of extracardiac systemic-to-pulmonary artery shunts, using many procedures such as Blalock–Taussig shunt procedure or its modification [modified Blalock–Taussig shunt (MBTS)], which is commonly used nowadays, modified Blalock–Thomas–Taussig shunt (commonly called the MBTS) is a surgical procedure used to increase pulmonary blood flow for palliation in duct-dependent cyanotic heart defects such as pulmonary atresia, which are common causes of blue baby syndrome. In this procedure, there is temporarily direction of the blood flow to the lungs and relieve cyanosis. Traditionally, these surgical procedures are accomplished by either a total intravenous anesthesia (TIVA) or inhalational-based anesthesia. The TIVA technique achieves hemodynamic stability but has many disadvantages such as increases in the period of mechanical ventilation and its associated complications, and increase in ICU stay. Although inhalational anesthetic-based technique may be associated with myocardial depression and dysarrythmias (up to ventricular arrhythmia), but, due to lower blood solubility, facilitates early awakening and endotracheal extubation; this technique decreases the duration of mechanical ventilation, ICU stay, and, therefore, total hospital stay. Patients and methods Forty ASA classes III and IV patients between 18 months and 6 years, scheduled for MBTS procedure for repairing CCHD, were to undergo systemic to pulmonary shunt using cardiopulmonary bypass (CPB) after median sternotomy. They were divided into two groups: patients in the TIVA group (n=20) were administered a combination of midazolam–fentanyl–propofol along with neuromuscular blockade, whereas the desflurane group (n=20) was administered desflurane with 0.6–1 MAC in 100% oxygen with a combination of fentanyl with neuromuscular blockade. Hemodynamic parameters [heart rate (HR), mean blood pressure], duration of elective ventilation, incidence of supraventricular tachycardia and ventricular tachycardia/ventricular fibrillation, and level of myocardial injury were detected by cardiac troponin I as a cardiac biomarker for myocardial injury recorded as primary outcome, whereas duration of inotrope use, ICU and hospital stay, and serum creatinine levels were recorded preoperatively, thereafter, at 24 h postoperatively, they were recorded as secondary outcome. Any serious adverse events, such as acute renal injury, or any other major cardiovascular/neurologic events were recorded. Results Repeated measure analysis was carried out to see the trend in HR from HR1 (at baseline) in both groups, HRs HR2 (just prior to CPB), HR3 (weaning from CPB), and HR4 (arrival at ICU) were significantly higher than HR1 (P<0.001). The mean arterial pressures recorded at time intervals where T2 (just prior to CPB) and T4 (arrival at ICU) were found to be significantly lower in patients included in the TIVA than in the desflurane group (P=0.003 and 0.002, respectively), but mean arterial pressure values at T1 (at baseline) and T3 (weaning from CPB) were insignificant in both the groups (P>0.05). Duration of mechanical ventilation, ICU stay and hospital stay were lower in the desflurane group compared with the TIVA group (P<0.005). While patients in the TIVA group recorded significantly lower inotrope use than those in the desflurane group (P<0.001). Likewise, the creatinine values measured at baseline and 24 h postoperatively were compared in both groups and also, inbetween group itself, were only significantly increased in the TIVA group (P=0.018). For cardiac troponin I levels, at T2 there were significantly higher than those at T1 in the TIVA group (P=0.001) when compared to the desflurane group (P=0.836). Conclusion TIVA has the advantage of hemodynamic stability, but it prolongs the duration of controlled ventilation and length of hospital stay. The current study demonstrated that a desflurane-based anesthetic provides comparable stability, early recovery of myocardial contractility, decreased duration of controlled ventilation, duration of ICU admissions, and total hospital stay.