Introduction: Monitoring cerebral perfusion in patients with brain injury is a major clinical challenge. Monitoring cerebral oxygenation (rSO2) via NIRS was introduced in the early 1980s, and many clinicians believed it to be a valuable method for assessing cerebral perfusion and subsequent measures to optimize cerebral flow. The main problem with the use of NIRS is the presence of intermediate structures—the skin, skull, meninges, cerebrospinal fluid—and their influence on the test result. Therefore, it seems that NIRS assessment performed on a patient during brain death can give an idea of the magnitude of the influence of these intermediate structures on the monitoring result. Case presentation: We present a case study of cerebral oxygenation measurements in a patient undergoing a brain death diagnostic procedure. A clinical situation in which cerebral blood flow is stopped can give an idea of the specificity of this method, in particular of the influence of intermediate structures on the monitoring result. In this case, the result obtained using NIRS is increased by the patient’s oxygenation before the apnea test. The influence of chromophores in the tissues surrounding the CNS and reflections and scattering of the light wave spectrum have a very significant effect on the final result of cerebral saturation measurement. Discussion: The majority of observations in existing research describing changes in cerebral perfusion or its optimization may be burdened by the problem described here, i.e., by the significant influence of measured intermediate structure oxygenation. The specificity of NIRS in assessing cerebral perfusion requires careful analysis. The therapeutic implications of monitoring cerebral oxygenation with NIRS are of great importance, and based on the example presented and the literature provided, this method should be used with caution. It has been shown that in a patient with brain death, the result of NIRS oxygenation measurements depends on the structures surrounding the brain.
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