The effects of activation of the lactoperoxidase (LPO) system by H2O2–NaSCN and hydrogen peroxide (H2O2) on the accessibility of sulphydryl groups (SH) in skimmed milk, and on the dynamic rheological properties of the resulting yoghurt were investigated. Four different concentrations of each reagent (20–80 mg H2O2–NaSCN/kg milk and 100–400 mg H2O2/kg milk) were compared. Clear negative correlations were noted between the accessibility of SH groups and both LPO activation rate and H2O2 concentration. Also the native PAGE pattern of the heat-treated samples showed that with increase in the H2O2–NaSCN and H2O2 concentrations, the level of interaction between β-lactoglobulin (β-lg) and κ-casein (κ-CN) decreased. The complex modulus (G*) of skimmed milk yoghurts declined gradually with the decrease in the concentration of accessible SH groups accordingly. Tan δ values of yoghurt samples were found to be different from the control, but close to each other, indicating that protein interaction forces taking place in the formation of gel networks of treated yoghurts were different from the control.