OBJECTIVE The aim of the study was to assess the efficacy of technetium 99m-methyl diphosphonate (Tc-MDP) and technetium 99m-methoxyisobutylisonitrile (Tc-MIBI) as radioaerosol alternatives to technetium 99m-diethylenetriaminepentacetate (Tc-DTPA) in the evaluation of pulmonary thromboembolism, as the direct consequence of the possible outcome could be cost saving. METHODS Patients referred to our institution from August 2015 to July 2017 for a ventilation-perfusion scan who fulfilled the inclusion criteria were enrolled into the study as participants. Each ventilation agent was used to ventilate 43 participants, making a total of 129 participants in the study. Images were assessed for quality and alveolar clearance qualitatively and semiquantitatively correspondingly by a nuclear medicine physician blinded to the agent used. RESULTS Tc-MIBI had higher count rates than Tc-DTPA and Tc-MDP, with a statistically significant difference when compared with Tc-DTPA (P=0.021). Tc-MIBI clearly showed slower alveolar clearance when compared with the clearance of Tc-DTPA (P≤0.0001) and Tc-MDP (P≤0.001). In terms of image quality, Tc-MIBI generally had better quality images as compared with the other two radioaerosols, with a statistically significant difference when compared with Tc-DTPA (P=0.001). CONCLUSIONS Tc-MIBI had superior image quality and slower alveolar clearance when compared with Tc-DTPA. Alongside Tc-MDP, these agents can replace Tc-DTPA whenever clinically and economically applicable.