Tumor hypoxia is generally considered to be related to aggressive behaviour of a tumor. As in lung cancer direct determination of oxygenation is difficult, hypoxia-related proteins have been studied. A number of studies on these proteins show different results and the usefulness of these protein expressions remains questionable. In this article, we relate one of these hypoxia-related proteins (hypoxia-inducible factor, HIF1a) to a direct in vivo spectroscopic measurement of tumor blood saturation performed during bronchoscopy. Seventeen samples from malignancies and non-malignant tissues were studied. Microvascular saturation levels in the no malignancy group equalled 87+/-11.5% (range 71-100%) and in the malignant group 43+/-21% (range 6-63%). This difference was statistically significant (p<0.0002). There was a significant difference in the spectroscopically determined saturations between the biopsies with negative expression of HIF1a and the biopsies with positive expression of HIF1a (p<0.005). From these data, it can be concluded that HIF1a expression is related to a low microvascular blood saturation as determined in vivo by optical spectroscopy. This study may lead to a better acceptance of the usage of different techniques to establish hypoxia in order to study the effect of hypoxia on therapeutic interventions and prognosis of lung cancer.