Transmission (Tx) scans are used in PET for attenuation correction (AC). For standalone PET this is typically done using Ge-68/Ga-68 sources, for PET-CT using CT. Therefore, standalone PET suffers from emission contamination during Tx scans, PET-CT does not. Here, we studied the effects of AC across the two systems. With a cylindrical phantom (Jaszczak Phantom, Data Spectrum Corp.) with hollow spheres (diameter 10-60 mm) two studies were performed. In the first study the hollow spheres were filled with 150 kBq/ml FDG and the background with 15 kBq/ml. In the second study we used 120 kBq/ml in the spheres and 50 kBq/ml in the background. Both a low and a high object-to-background ratio are studied this way. Multiple scans were acquired on a standalone PET and a PET-CT until 1% of the initial concentration remained. Activity concentration in the spheres and background was measured from the reconstructed images and compared to the actual concentration. For standalone PET, emission scans were reconstructed using hot Tx (emission contaminated) and cold Tx (not contaminated). Uniformity within the spheres was investigated by profile analysis. For PET-CT, the concentration in the big spheres (> 16 mm) was recovered. For the smaller spheres, recovery was insufficient due to partial volume effects. For standalone PET the recoveries of the spheres (> 16 mm) were 20% (first study) and 13% (second study) lower than the actual concentration. Using hot Tx, underestimation of activity concentration was up to > 50%. Nonuniformities within the biggest spheres were up to 35%, 12%, and 5% (first study), using standalone PET with hot Tx, cold Tx, and using PET-CT, respectively. Due to contamination of AC by emission photons, standalone PET results in a bias in the activity concentration and uniformity. Especially when patients get follow-up PET scans on both standalone PET and PET-CT, this may lead to misinterpretation.