The 13C-urea breath test is a noninvasive analysis for the detection of Helicobacter pylori infection and is valuable for judging the effects of antimicrobial treatment. Up to date the most popular technique for 13C-urea breath test: UBT, is performed by collecting expired gas into an aluminum bag, but the result is considered to be influenced in the diagnosis of Helicobacter pylori infection by the existence of anatomical dead space gas. We therefore introduced a new technique to measure 13CO2 and 12CO2 continuously during expiration, identified the correct alveolar gas, and excluded the effect of anatomical dead space. Subjects were 127 males and 8 females. We compared the diagnostic accuracy of these aluminum bag and continuous measurement methods. We adopted serological IgG positive and barium-meal study positive cases as a gold standard for the diagnosis. Diagnostic accuracy by continuous measurement was superior to that by the aluminum bag method. We should pay attention to the existence of anatomical dead space for accurate diagnosis. Continuous measurement is important in the collection of end tidal expired gas in order to make an accurate diagnosis.