Background: Menicon Z night orthokeratology (OK) lenses was introduced in Malaysia in 2015 and to date there is no report on its effects on the cornea. The objective of this study was to examine short term changes in corneal thickness and morphology of endothelial cells in young Malay adults after wearing Menicon Z night OK lenses. Methods: Corneal thickness was measured at the central and mid-peripheral locations of 20 participants aged 22.45±1.19 years using Tomey SP-3000 A-scan ultrasonography. Endothelial images of the central and peripheral locations captured using Tomey EM-3000 specular microscope were noted. Corneal thickness, endothelial cell density (ECD), coefficient of variation in cell size (CV), and hexagonality (HEX) at baseline, 24 hours, three months and six months after treatment were noted and analysed using repeated measure analysis of variance. Results: Central corneal thickness decreased significantly over a three-month period (p=0.001) and stabilised thereafter. There were no significant changes in thickness in all peripheral areas measured (p>0.05), and in ECD, CV and HEX after the six-month period (p>0.05). Conclusions: The current study showed that significant thinning of central cornea and none at the mid-periphery. OK lens wear with Menicon Z night lenses had no effects on corneal morphology over the six month period.