Toluene dioxygenase-catalysed (TDO) oxidation converts substituted phenol substrates into catechols, hydroquinones, and chiral cyclohexenone cis-diol products. The ratio between the isolated products varied widely even between similar substrates, e.g. o-cresol, m-cresol and p-cresol. These differences are caused by different binding interactions within the active site of TDO. This study provides insight into the binding interactions by molecular docking using AutoDock tools. The nature of binding of phenolic substrates was of major interest, in order to explain the observed regio- and stereo-selectiviy of product formation. The ellipse-shaped binding pocket of TDO consists of a polar and a hydrophobic region, limiting the possible substrate orientations. The phenolic hydroxyl group was preferentially hydrogen bonded with Gln-215 and His-311 in the active site. In some cases, a hydrogen bond was formed with other amino acids, e.g. Asp-219and Met-220, instead. The position and type of the substituent on the phenol ring influences the formation of transient intermediates, and thus the nature and stability of the major isolated product.