BACKGROUND: During bilateral transthoracic endoscopic sympathicotomy (TES), we have noticed a tendency for hypoxemia during deflation of the second lung despite adequate reinflation of the first one. This study was designed to compare PaO2 during TES of the first side with that of TES of the second side and to investigate whether PaO2 during the sequential one-lung ventilation (OLV) was correlated with two-lung ventilation (TLV) time after reinflation of the collapsed first lung. METHODS: Forty patients were randomly allocated into two groups. After TES of the first side, OLV of the second side was immediately performed after reinflation of the collapsed first lung (group A), or after 10 minutes of TLV when switching between the operated sides (group B). Arterial blood gas samples were taken at TLV before surgery, at 2 minute intervals during OLV, and during the period of TLV when switching between the operated sides. RESULTS: In group A, the significantly decreased PaO2 was observed during TES of the second side compared with TES of the first side (P < 0.01). In group B, there was no significant difference in PaO2 except 2 minutes after OLV. PaO2 during TLV and 4 and 6 minutes after OLV of the second side TES in group A significantly decreased compared with those of group B (P < 0.05). The lowest PaO2 during OLV of the second side TES was significantly lower in group A (93.5 +/- 28.7 mmHg) than in group B (154.1+/- 48.3 mmHg). CONCLUSIONS: A significantly decreased PaO2 was observed during TES of the second side, compared with TES of the first side, and time was needed after lung collapse for its full oxygenation function to recover.