The purpose of this study was to examine the effect of energy threshold selection on the quantification of contrast agents in photon-counting CT (PCCT). A phantom was devised consisting of vials of iodine (4, 8, 16 mg/mL), gadolinium (4, 8, 16 mg/mL), and bismuth (5, 10, 15 mg/mL) within a cylindrical water container. The phantom was scanned on a prototype photon-counting CT scanner. The detected photons were binned into two energy bins using a fixed lower threshold of 20 keV and an upper threshold that varied between 50 to 90 keV. An image containing all the spectral information (threshold 1) was examined along with both binned images. Images were evaluated for the mean and standard deviation of CT number in each vial and contrast-to-noise ratio (CNR) for each concentration. CT number values in the threshold 1 image remained mostly unchanged as energy threshold was increased. Vials of iodine and gadolinium had slightly higher CT numbers in lower energy bin images than the threshold 1 images, but the percentage difference varied slightly (6-37% for iodine and 5-22% for gadolinium) with energy threshold. In higher energy bin images, CT numbers were lower (20-68% for iodine and 10-59% for gadolinium) than threshold 1 and the difference decreased with increasing energy threshold. For bismuth, the percentage difference in the lower bin decreased (by 11-19%) with energy level while it increased (by 18-23%) in the upper bin. CNR varied only slightly in the lower energy bins and decreased with increasing energy threshold for all materials.