Objective To evaluate the differences in central corneal thickness, curvature and endothelium between patients wearing soft contact lenses (SCL) and those wearing rigid gas permeable contact lenses (RGPCL). Methods Three hundred eyes of 172 patients with no eye disorders except ametropia were divided into two groups: SCL group and RGPCL group. All patients had to wear contact lenses at least 6 hours a day. Corneal thickness, corneal endothelium, corneal curvature and topography were measured and comparisons were made between baseline measurements and the measurements taken at various intervals: before wearing, 6 months, and 3 years after wearing the contact lenses. Results Central corneal thickness after 3 years of SCL wear was (27.1±-0.8)mm less than before wearing the SCL (P＜0.05); central corneal thickness after 3 years of RGPCL wear was (3.1±2.2)mm less than before wearing the RGPCL (P＞0.05), but there were no differences between the SCL and RGPCL groups prior to and 6 months after the lenses wear (P＞0.05). However, there were obvious differences at 3 years (P＜0.05). There were no obvious differences in corneal curvature in the SCL group (P＞0.05). But more differences betweeen wearing before and 3 years after in RGPCL group. The corneal endothelium in the SCL group was partially reduced (368.5±31.5)cells/mm2 and (140.2±5.6)cells/mm2 was reduced in the RGPCL group, there was a significant differencesbetween the 2 groups (P＜0.05). Conclusion This study shows that RGPCL affect the corneal endothelium less. Therefore, RGPCL can be worn safely over the long term.