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Biodegradation of petroleum hydrocarbon contamination is a common method for remediating soils and groundwater. Due to complexities with field-scale studies, biodegradation rates are typically evaluated at the bench-scale in laboratory studies. However, important field conditions can be difficult to mimic in the laboratory. This study investigates three scaling factors that can impact laboratory biodegradation rates and that are frequently unaccounted for in typical laboratory experimental procedures. These factors are soil heterogeneity, morphology of petroleum hydrocarbon non-aqueous phase liquids (NAPLs) and soil moisture distribution. The effects of these factors on the biodegradation rate of diesel NAPL is tested under a variety of experimental procedures from well-mixed batch studies to four-foot static soil columns. The results indicate that a high degree of variability results from even small-scale heterogeneities. In addition, it appears that as the experimental scale increases, the measured biodegradation rates slow. The results indicate that diesel biodegradation rates derived from small-scale experiments are not necessarily representative of field-scale biodegradation rates.