We herein report the first case of fatal extensive bone cement embolism appearing in pulmonary arterioles following surgical vertebral screw augmentation, which histological evidence of bone cement emboli was confirmed by Fourier transform infrared spectroscopy. A 47-year-old woman has accepted multilevel spine fusion and pedicle screw augmentation with totally 4 ml bone cement infusion. She suddenly developed low blood pressure, dyspnoea, and unconsciousness approximately 1 h post anaesthetic recovery, and then she was dead. It was shown both lungs were edematous in autopsy, and bluish emboli were appeared in extensive pulmonary arterioles in H&E stained sections. Negative information was shown in Molybdenum target X-ray imaging, but the emboli were confirmed to be PMMA bone cement by Fourier transform infrared spectroscopy. The present case indicated it might be effective to confirm the dubious trace component in histology by FTIR.