Objective In this study, we investigated the optimal reconstruction algorithm in fluorodeoxyglucose (FDG) positron emission tomography (PET) with a short acquisition time. Materials and Methods In the phantom study, six spheres filled with FDG solution (sphere size: 6.23-37 mm; radioactivity ratio of spheres to background = 8:1) and placed in a National Electrical Manufacturers Association phantom were evaluated. Image acquisition time was 15 to 180 seconds, and the obtained image data were reconstructed using each of the Fourier rebinning (FORE) + ordered subsets expectation-maximization (OSEM) and 3D-OSEM algorithms. In the clinical study, mid-abdominal images of 19 patients were evaluated using regions of interest placed on areas of low, intermediate, and high radioactivity. All obtained images were investigated visually, and quantitatively using maximum standardized uptake value (SUV) and coefficient of variation (CV). Results In the phantom study, FORE + OSEM images with a short acquisition time had large CVs (poor image quality) but comparatively constant maximum SUVs. 3D-OSEM images showed comparatively constant CVs (good image quality) but significantly low maximum SUVs. The results of visual evaluation were well correlated with those of quantitative evaluation. Small spheres were obscured on 3D-OSEM images with short acquisition time, but image quality was not greatly deteriorated. The clinical and phantom studies yielded similar results. Conclusion FDG PET images with a short acquisition time reconstructed by FORE + OSEM showed poorer image quality than by 3D-OSEM. However, images obtained with a short acquisition time and reconstructed with FORE + OSEM showed clearer FDG uptake and more useful than 3D-OSEM in the light of the detection of lesions.