Individuals with sickle cell disease (SCD) may have oxyhaemoglobin desaturation during the steady-state, the causes of which are incompletely known. We studied a cohort of 585 children who have sickle cell anaemia (SS), sickle beta0-thalassaemia (Sbeta0), sickle-haemoglobin C disease (SC), or sickle beta+-thalassaemia (Sbeta+) to determine the relationships between steady-state oxyhaemoglobin saturation (SpO2) and SCD genotype, age, gender, steady-state haemoglobin (Hb) and reticulocyte count, and rate of acute chest syndrome (ACS). The SS/Sbeta0 group (n = 390) had lower mean SpO2 than the SC/Sbeta+ group (n = 195) (96.3% vs. 98.7%, P < 0.001). Among SS/Sbeta0 subjects, a decrease in steady-state SpO2 correlated with a decrease in Hb, an increase in reticulocytes, older age and male gender. These correlations were not found in the SC/Sbeta+ group. Prior ACS did not correlate with steady-state SpO2. A multivariate model explained 45% of the variability in SpO2, but only 5% of the variation in SpO2 was explained by Hb. We conclude that steady-state desaturation is common in individuals with SCD, but it appears to be unrelated to prior episodes of ACS and largely unexplained by chronic anaemia.