Obstructive Sleep Apnea Syndrome (OSAS) may contribute to the increasing frequency of metabolic disorders. Intermittent hypoxia (IH) is a major characteristic of the syndrome. However, the existing indices of hypoxia in sleep cannot express accurately the effect of the mild desaturations. In this study, a total of 51 patients without other comorbidities were examined by polysomnography (PSG). Hypoxia parameters were analyzed, in the intervals with low values of SpO2 signal. More specifically, the thresholds were set at 94 and 92% and the average value (M) of the SpO2 signal, in areas below thresholds, were calculated. Moreover, the desaturations were analyzed, together with their duration within the recording in terms of SpO2signal parameters. The patients’ blood sample was analyzed for metabolic parameters. In total, 28 individuals were diagnosed with severe OSAS, (Apnea Hypopnea index (AHI) 59.11 ± 26.10/h, averSpO2 91.64 ± 4.50%, minSpO2 78.18 ± 10.26%, t < 90 21.42 ± 28.64 and ODI 35.48 ± 33.79/h). A statistically significant correlation between the average M92 value with insulin levels (r = 0.401, p < 0.03) and homeostasis model assessment (HOMA) (r = 0.431, p < 0.022) was displayed. Likewise, a correlation between the amount of desaturations and fasting glucose (r = 0.400, p < 0.035) was observed. Moreover, a statistically significant correlation between the desaturations’ average value with insulin (r = 0.378, p < 0.047) and CRP (r = 0.400, p < 0.035) levels was also revealed. A strong correlation also emerged from the cumulative desaturations’ duration as recorded by the SpO2 signal with fasting glucose levels (r = 0.964 p < 0.001), glycosylated hemoglobin (r = 0.860, p < 0.000) and HOMA index (r = 0.580, p < 0.001). The results suggest that the Hypoxia factors derived from SpO2 signal analysis, are strongly correlated with the insulin resistance and with fasting glucose levels. The correlations of the proposed hypoxia parameters were found to be stronger than the already known hypoxia indices, deriving from the PSG, however a more extended analysis is necessary in order to consolidate the findings of this study.