Penetration of oral bacteria through root fillings leads to their long term failure. Dimensionally stable alkaline cements have been developed. A saliva challenge model was used to compare resistance to bacterial penetration of these alkaline cements to conventional root fillings that combine gutta percha (GP) with epoxy resin sealers. A sample of 140 human roots with single straight canals prepared to standard length and canal size were obturated with mineral trioxide aggregate (MTA) (Nex MTA or MTAmix), with an alkaline calcium hydroxide hard setting cement (Supercal), or with GP and a resin cement (either AH-Plus or Zirmix). Negative control roots were sealed with wax, while positive controls were left open. The test assemblies were gamma sterilised, then the coronal root face was exposed daily to fresh stimulated human saliva diluted in broth. Bacterial penetration was determined by assessing growth in sterile brain-heart infusion (BHI) medium in contact with the root apex. Using Kaplan-Meier survival analysis, in order of performance from highest to lowest: Negative control, Supercal, Nex MTA, Zirmix, MTAmix, GP + AH-Plus, and the positive control. In addition, statistically significant differences were noted between Supercal and AH-Plus, and between the two MTA cements. It can be concluded that alkaline cements, particularly Supercal, can show considerable resistance to bacterial penetration from constant saliva challenge, and provide superior sealing ability in comparison to resin cements. While this property is due mostly to dimensional stability, the release of hydroxide ions could be a contributing factor to impaired bacterial survival, and this aspect should be explored further.