The physiological status of anesthetized rats greatly influences blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI). Monitoring of physiological parameters, particularly partial pressure of carbon dioxide (pCO(2)) levels in the blood, is therefore an important part in the design and performance of reliable fMRI experiments. In this paper, the use of a transcutaneous blood gas analyzing system in rats as a completely noninvasive and MR-compatible method is demonstrated. It was successfully used to monitor continuously pCO(2) values, as an effective alternative to more invasive methods, such as analysis of repetitive arterial blood samples or endtidal capnography. In addition, the transcutaneous pCO(2) of rats anesthetized for long periods was studied using different anesthetic substances and experimental protocols. On-line monitoring of pCO(2) values permitted experimental conditions to be established in which the animals remained normocapnic and during which a robust and consistent BOLD contrast could be observed upon somatosensory forepaw stimulation. A transcutaneous pCO(2) threshold level was defined for the reliable detection of a stimulus-dependent BOLD response.