Objective: The modified Blalock-Taussig shunt (mBTs) is used palliatively in cyanotic congenital heart diseases when definitive surgery is not possible. However, factors contributing to shunt thrombosis and in-hospital mortality in infancy remain unclear. The present study aimed to identify those risk factors. Materials and Methods: The authors conducted a retrospective review of medical records from the infants diagnosed with cyanotic congenital heart disease who underwent isolated mBTs procedures at Chiang Mai University Hospital between March 1, 2011 and April 30, 2015. Patient characteristics, operative data, and treatment outcomes were extracted. The primary outcome assessed was shunt thrombosis, with in-hospital mortality within 30 days as the secondary outcome. Risk regression analysis was used to identify factors associated with both outcomes. Results: Forty-nine infants were included in the present study, with a mean weight of 3.81 kilograms (range of 2.05 to 7.70 kg) and an average age of 66 days (range of 3 to 349 days). Early shunt thrombosis occurred in eight patients (16.33%), and five patients (10.2%) died. Multivariable analysis revealed only sepsis as a significant predictor (RR 7.93, 95% CI 1.86 to 33.69). Neither weight at surgery nor shunt size showed a significant association with shunt thrombosis. Prognostic factors for in-hospital mortality in the univariable analysis included prematurity (p=0.01), size of pulmonary artery (p=0.033), preoperative intubation (p=0.043) shunt thrombosis (p=0.002), and body weight at surgery of less than 3 kg (p=0.002). However, multivariable analysis could not demonstrate any difference. Conclusion: Postoperative sepsis emerged as the sole statistically significant predictor for early shunt thrombosis following isolated mBTs. However, larger studies are needed to ascertain prognostic factors for in-hospital mortality in infants with cyanotic congenital heart disease.