BACKGROUND: Percutaneous mechanical aspiration thrombectomy is increasingly being employed as a less invasive alternative for managing right heart masses, including clot in transit. AIMS: We aimed to analyze trends in the use of catheter-directed aspiration (CDA) for right heart masses. Additionally, we analyzed in-hospital outcomes of percutaneous versus surgical approaches for patients with CIT and PE. METHODS: We performed a retrospective cohort study based on the National Inpatient Sample (NIS) database from 2016 to 2020. Our population included patients who underwent catheter-directed mechanical aspiration of right heart mass and thrombus to analyze trends during the study period. Moreover, we identified patients with acute PE stratified into cohorts: percutaneous catheter-directed thrombectomy (CDT) and surgical embolectomy. The primary outcome was the composite endpoint of in-hospital mortality, major bleeding, and stroke. RESULTS: A total of 1789 underwent CDA during the study period. There was an increase in usage of CDA for right heart thrombus and mass (203 in 2016 vs. 533 in 2020). Among patients with PE, 400 patients underwent CDT, and 150 patients underwent SE for clot in transit. On multivariate analysis, there was no significant difference in composite endpoints between the two groups (31.2% in percutaneous vs. 40% in the surgical group, p = 0.243). However, patients who underwent CDT had lower in-hospital mortality than surgical thrombectomy (12.5 vs. 26.6%, p = 0.015). CONCLUSIONS: There is a significant increase in the use of CDA for right heart thrombus and mass. Moreover, our study shows significantly lower in-hospital mortality in PE patients with CIT undergoing CDT compared to surgical thrombectomy.