This study investigated the dentinal tubule penetration of mineral trioxide aggregate (MTA), NeoMTA Plus and Biodentine placed by either manual condensation or ultrasonic activation in simulated open apex model. Standardized divergent open apex models were created using palatal roots of 60 human maxillary molars and divided into six groups according to the used cements and activation methods (n = 10): MTA-manual condensation, MTA-ultrasonic activation, NeoMTA Plus-manual condensation, NeoMTA Plus-ultrasonic activation, Biodentine-manual condensation, Biodentine-ultrasonic activation. For the measurement of penetration, the cements were mixed with 0.1% Rhodamin B and 6-mm apical portions of each root canal were obturated in an orthograde direction. The roots were embedded into acrylic blocks, and 1-mm-thick sections were obtained at 3 mm from the apex. Specimens were mounted onto glass slides and scanned under a confocal laser scanning microscope (CLSM) and stereomicroscope. Dentinal tubule penetration areas, depth and percentage were measured using LSM and ImageJ software. The data were analyzed using two-way analysis of variance (anova) with Bonferroni correction (alpha = 0.05). No correlation was found between stereomicroscope and CLSM analyses (p > .05). CLSM analysis showed no significant differences between MTA, NeoMTA Plus, and Biodentine groups when manual condensation was used (p > .05). Ultrasonic activation did not increase the tubular penetration of MTA, NeoMTA Plus or Biodentine as compared to manual condensation of each material (p > .05). MTA, NeoMTA Plus and Biodentine showed similar tubular penetration when manual condensation was used. Ultrasonic activation of these cements had no effect on tubular penetration of each material as compared to the manual condensation counterparts.