The measurement of average alveolar expired Pco(2) (PAECO(2)) weights each Pco(2) value on the alveolar plateau of the CO2 expirogram by the simultaneous change in exhaled volume. PAECO(2) can be determined from a modified analysis of the Fowler anatomic dead space (VDANAT). In contrast, end-tidal PCO2 (PETCO(2)) only measures PCO2 in the last small volume of exhalate. In conditions such as mechanical ventilation with positive end-expiratory pressure (PEEP), where the alveolar plateau can have a significant positive slope, we questioned how much PETCO(2) could overestimate PAECO(2). Accordingly, in six anesthetized ventilated dogs, we digitally measured and processed tidal PCO2 and flow to determine VDANAT. We determined PETCO(2) and PAECO(2) before and after the application of 7.6 cm H2O PEEP. Alveolar dead space to tidal volume fraction (VD/VT) was determined by [arterial Pco,alveolar PCO2]/arterial PCO2, where alveolar PCO2 was determined by either PETCO(2) or PAECO(2). During baseline ventilation, PETCO(2) was 3.4 mm Hg (approximately 11%) greater than PaECO(2). Because PEEP significantly increased the slope of the alveolar plateau from 28 to 74 mm Hg/L, the difference between PETCO(2) and PAECO(2) significantly increased to 6.6 mm Hg (approximately 20% difference). THe concurrent increase in VDANAT during PEEP decreased alveolar tidal volume and tended to limit the overestimation of PETCO(2) compared to PAECO(2). When alveolar PCO2 was estimated by PETCO(2), alveolar VD/VT was 18%, compared to an alveolar VD/VT of 26% when alveolar PCO2 was estimated by PAECO(2). This difference was significantly magnified during PEEP ventilation. The overestimation of PAECO(2) by PETCO(2) can result in a falsely high assessment of overall alveolar PCO2. Moreover, the use of PAECO(2) to estimate alveolar PCO2 in the determination of the alveolar dead space fraction can result in falsely low and even negative values of alveolar dead space.