The aim of this study was to evaluate the sealing ability and marginal adaptation of calcium silicate-based cements (CSCs) in root-end cavities prepared by ultrasonic and laser tips. A total of 72 extracted human maxillary incisor teeth were randomly divided as 60 teeth in experimental groups and 6 teeth each for positive and negative control groups. Specimens in experimental groups were obturated, their root-end resections were performed and randomly divided into six groups (n=10) as follows: G1: Ultrasonic retrotip+MTA, G2: Ultrasonic retrotip+Calcium Enriched Mixture (CEM), G3: Ultrasonic retrotip+Biodentine, G4: Er:YAG laser tip+MTA, G5: Er:YAG laser tip+CEM, G6: Er:YAG laser tip+Biodentine. The sealing ability was measured by fluid transport method. Six specimens from each experimental group were randomly selected to analyze marginal adaptation and prepared for scanning electron microscopy (SEM) analysis. Micrographs were scored and also analyzed using Image J software. Data were analyzed with; two-way ANOVA, Bonferroni, Kruskall-Wallis, Mann-Whitney-U, Siegel & Castellan, and Spearman correlation coefficient tests. No significant difference was found between materials regarding the sealing ability and marginal adaptation (p>0.05). Significantly greater fluid movement and poor marginal adaptation were seen for materials placed in cavities prepared by laser tips (p<0.05). Positive correlation was found between the results of scoring and Image J analysis of SEM images (r=0.596, p<0.001). Fluid transport method and SEM analysis gave similar results suggesting the use of ultrasonic-retrotips for preparing root-end cavities which are going to be filled with one of these CSCs.