The use of hydraulic silicate cements (HSCs) for vital pulp therapy has been found to release calcium and hydroxyl ions promoting pulp tissue healing and mineralized tissue formation. The present study investigated whether HSCs such as mineral trioxide aggregate (MTA) affect their biological and antimicrobial properties when used as long-term pulp protection materials. The effect of variables on treatment outcomes of three HSCs (ProRoot MTA, OrthoMTA, and RetroMTA) was evaluated clinically and radiographically over a 48-78 month follow-up period. Survival analysis was performed using Kaplan-Meier survival curves. Fisher's exact test and Cox regression analysis were used to determine hazard ratios of clinical variables. The overall success rate of MTA partial pulpotomy was 89.3%; Cumulative success rates of the three HSCs were not statistically different when analyzed by Cox proportional hazard regression analysis. None of the investigated clinical variables affected success rates significantly. These HSCs showed favorable biocompatibility and antimicrobial properties in partial pulpotomy of permanent teeth in long-term follow-up, with no statistical differences between clinical factors.