To compare the effect of three different phakic intraocular lenses (pIOLs) on the corneal endothelial cell density (ECD). This was a prospective observational cohort study that included 60 eyes (30 patients) with axial myopia of -6.50 to -22.00 diopters (D). The Verisyse anterior chamber (AC) rigid iris fixated pIOL, the Veriflex (AC) flexible iris fixated pIOL, and the Visian posterior chamber (PC) implantable collamer lens (ICL) were implanted in three equal groups of patients. The effect of the three pIOLs on the ECD was compared over a follow-up period of one week, and one, three, and six months, and one, two, and three years. Specular microscopy was done to evaluate the cornea before the surgery and throughout the study. Changes were statistically analyzed and compared. In the first three postoperative months, Verisyse and Veriflex pIOLs induced almost the same amount of endothelial cells loss of 10.3% and 10.6%, respectively, while ICLs showed endothelial cells loss of 3.5%. At the end of the three-year study, Veriflex pIOLs induced the highest rate of endothelial cell loss of 25%, while Verisyse and ICL lenses showed endothelial cells loss of 15.7% and 13.4%, respectively. The main effect of time and type of lens was statistically significant (p<0.001). All pIOLs cause a decrease in ECD. The AC pIOLs tend to be associated with more cell loss than PC pIOLs. Surgical insult is the important factor responsible for the early endothelial cell loss, while the material from which the pIOL is made may be an important factor for the continuous corneal endothelial cell loss over a long time.