The diagnosis of ventilator-associated pneumonia has been clouded by uncertainty, because a reference standard has never been established. The use of invasive procedures to obtain respiratory tract samples for culture, with quantitation of the bacteria isolated, has been the approach most commonly advocated. Quantitation of bacteria from lower respiratory tract specimens can be used to distinguish colonization from infection. We review the invasive procedures (bronchoalveolar lavage, protected specimen brushing, nonbronchoscopic bronchoalveolar lavage, and blinded bronchial sampling), the methods of quantitation used, the types of catheters used, the sample collection methods, and the criteria used as cutoffs for the quantitative cultures. Quantitation of lower respiratory tract samples is inherently unstable from a mathematical perspective, given the variability in the volume of fluid instilled and reaspirated and the magnitude and complexity of the area being sampled. We also briefly review the use of quantitation for bacterial infections other than pneumonia, including urinary tract infection and catheter-related bacteremia. The variability in both the methods and reference criteria in the studies reviewed show that the quantitation approach is neither standardized nor evidence based.