Objective: This study was carried out to understand whether Q.Clear and ordered subset expectation maximization (OSEM), reconstruction algorithms used in fluorine-18-fluorodeoxyglucose (F-18-FDG) positron emission tomography/computed tomography (PET/CT) applications, and parameters such as time offlight (TOF) and point spread function (PSF) cause different results in semi-quantitative measurements. Subjects and Methods: Raw PET data of 264 patients who were referred to F-18-FDG PET/CT imaging with the purpose of evaluation of known or suspicious malignant disease were reconstructed separately with Q. Clear (GE Healthcare), a BPL, an OSEM algorithm, PSF (SharpIR degrees) and TOF (VUE Point FX degrees) methods. Each patient's liver, mediastinal blood pool, metabolic tumor volume (MTV), total lesion glycolysis (TLG), and standardized uptake values (SUV) (SUVmax, SUVmean, and SUVpeak) of a total of 264 lesions selected from the patients were performed. Results: (3350+ToF yielded higher measurement results than all other variables for all of the lesion SUVmax, lesion SUVmean, L/AP SUVmax, and L/AP SUVmean parameters. OSEM+ToF and OSEM+TOF+PSF algorithms yielded higher mean and median SUVmax values for the reference structures (liver and mediastinum) and for lesions SUVmax and SUVmean values were statistically significantly lower than the (3 350+ToF method. The method with the lowest mean value for the L/Liver SUVmax variable was OSEM+ToF 4iter16ss (mean=1.76), while the method with the highest mean value was (3350+ToF (mean=2.26). (3 350+ToF was the reconstruction method with the highest ratios for L/AP SUVmax and SUVmean for both lesions below and above 1cm. 13350 + ToF algorithm had also statistically significantly higher results for these variables compared to all other parameters in malignant lesions. Conclusions: When comparing(18)F-FDG PET/CT images, the use of different reconstruction algorithms may lead to misleading results, especially in the evaluation of response to treatment of malignancies.