In 2018, an expert panel recommended two key modifications to the most used algorithm for screening neonates for critical congenital heart disease (CCHD). Our aim was to evaluate the outcomes of the modified algorithm compared to those of the original algorithm in a real-world setting. We compared the performance characteristics of an original CCHD algorithm used to screen term neonates at a large hospital system between October 26, 2018 and the recommended modified algorithm used between October 15, 2020 and June 30, 2022. We calculated sensitivity, specificity, false positive rate, proportion of false positives with non-CCHD illness, and error rates of test administration and interpretation for each algorithm. Sensitivity was not significantly different betweenthe modified algorithm compared to the original algorithm (40.00% vs 12.50%, p-1.00), but specificity was lower (and hence false positive rate higher) in the modified algorithm (99.91% vs. 99.98%, p<0.001). Despite a higher false positive rate in the modified algorithm, the proportion of false positives with significant non-CCHD illness was similar (36.47% vs. 28.57%, p=1.00), a finding that translated to an increase in number of cases of significant non-CCHD illness detected (11 cases out of 32,178 screens vs. 2 cases out of 32,984 screens). Error rates of test administration and interpretation were similar between the two algorithms. In this limited study, the modified algorithm for CCHD screening using pulse oximetry had a higher false positive rate than that of the original AAP algorithm.However, this higher rate led to an increased overall number of cases detected of significant non-CCHD illness.