In many applications of silicon epitaxial layers grown on silicon substrates it is necessary to oxidize the substrate and then remove the oxide prior to epitaxial deposition. This oxidation step is found to produce a greatly increased density of stacking faults in the deposit. This anomalous increase in stacking faults can be eliminated if the back (undeposited) substrate surface is treated either to abrasive processes such as lapping and scribing or to a boron‐gettering process prior to oxidation. Both types of treatment are likewise found to eliminate saucer‐like pits observed in oxidized slices after structural etching. The incidence of these pits is closely correlated with the incidence of stacking faults in the grown layer. It is concluded that the pits represent precipitates of fast‐diffusing impurities and are probable nucleation sites for stacking faults.