Filtered back-projection (FBP) is the most commonly used reconstruction method for PET images, which are usually noisy. The iterative reconstruction segmented attenuation correction (IRSAC) algorithm improves image quality without reducing image resolution. The standardized uptake value (SUV) is the most clinically utilized quantitative parameter of [fluorine-18]fluoro-2-deoxy-D-glucose (FDG) accumulation. The objective of this study was to obtain a table of SUVs for several normal anatomical structures from both routinely used FBP and IRSAC reconstructed images and to compare the data obtained with both methods. Twenty whole-body PET scans performed in consecutive patients with proven or suspected non-small cell lung cancer were retrospectively analyzed. Images were processed using both IRSAC and FBP algorithms. Nonquantitative or gaussian filters were used to smooth the transmission scan when using FBP or IRSAC algorithms, respectively. A phantom study was performed to evaluate the effect of different filters on SUV. Maximum and average SUVs (SUVmax and SUVavg) were calculated in 28 normal anatomical structures and in one pathological site. The phantom study showed that the use of a nonquantitative smoothing filter in the transmission scan results in a less accurate quantification and in a 20% underestimation of the actual measurement. Most anatomical structures were identified in all patients using the IRSAC images. On average, SUVavg and SUVmax measured on IRSAC images using a gaussian filter in the transmission scan were respectively 20% and 8% higher than the SUVs calculated from conventional FBP images. Scatterplots of the data values showed an overall strong relationship between IRSAC and FBP SUVs. Individual scatterplots of each site demonstrated a weaker relationship for lower SUVs and for SUVmax than for higher SUVs and SUVavg. A set of reference values was obtained for SUVmax and SUVavg of normal anatomical structures, calculated with both IRSAC and FBP image reconstruction algorithms. The use of IRSAC and a gaussian filter for the transmission scan seems to give more accurate SUVs than are obtained from conventional FBP images using a nonquantitative filter for the transmission scan.