Study Objectives: The aim of this study was to compare the oxygen desaturation index (ODI) generated by two different sleep software systems. Methods: Participants undergoing diagnostic polysomnography for suspected obstructive sleep apnea underwent simultaneous oximetry recording using the ResMed ApneaLink Plus device (AL) and Compumedics Profusion PSG3 system (Comp). The ODI was calculated by the algorithms in the respective software of each system. To determine if differences were due to algorithm or recording devices, the Comp software was also used to generate ODI values using oximetry data from the AL. Results: In 106 participants, there was good correlation but poor agreement in the ODI generated by the two systems. AL ODI values tended to be higher than Comp ODI values, but with significant variability. For ODI4%, bias was 4.4 events/h (95% limits of agreement −5.8 to 14.6 events/h). There was excellent correlation and agreement when the same oximetry raw data was analyzed by both systems. For ODI4%, bias was 0.03 events/h (95% limits of agreement −2.7 to 2.8 events/h). Similar results were evident when the ODI3% was used. Conclusions: There is a clinically significant difference in ODI values generated by the two systems, likely due to device signal processing, rather than difference in ODI calculation algorithms.