Large sensitivity increases are realized in positron emission tomography when the interplane septa are removed and all lines of response acquired. Unfortunately, three-dimensional acquisition results in a large increase in scatter fraction which prevents accurate quantitation. By acquiring short two-dimensional scans prior to three-dimensional ones, scatter distributions can be estimated from differences between lines of response common to both datasets. This initial scatter distribution can be further modified to approximate scatter in the entire three-dimensional dataset. The method was validated with phantom measurements in which absolute activity concentrations were known in all compartments. Following scatter correction, a four-compartment phantom that was nonuniform in activity and density, both axially and transaxially, gave activity concentrations of 0.45 +/- 0.02, 0.31 +/- 0.02, 0.01 +/- 0.01 and 0.01 +/- 0.01 microCi/cc for compartments containing 0.43, 0.29, 0.0 (air) and 0.0 (water) microCi/cc, respectively. Thus, scatter distributions for complex sources can be estimated from image data without lengthy Monte-Carlo simulations. When activity distributions vary slowly with time, this method can be used to correct for scatter in three-dimensional patient studies.