The purpose of this study was to evaluate elasticity and viscoelasticity in the anterior and deeper stromal regions of the cornea after cross linking with three different protocols using atomic force microscopy (AFM) through indentation. A total of 40 porcine corneas were used in this study and were divided into 4 groups (10 corneas per group): control (no treatment), Dresden (corneal epithelial debridement, riboflavin pretreatment for 30 minutes and a 3mw/cm2 for 30 minutes UVA irradiation), accelerated (corneal epithelial debridement, riboflavin pretreatment for 30 minutes and a 30mw/cm2 for 3 minutes UVA irradiation), and genipin (corneal epithelial debridement and submersion of anterior surface in a 1% genipin solution for 4 hours). Elasticity and viscoelasticity were quantified using AFM through indentation for all corneas, for the anterior stroma and at a depth of 200μm. For the control, Dresden, accelerated, and Genipin groups, respectively, the average Young’s modulus for the anterior stromal region was 0.60±0.58MPa, 1.58 ±1.04MPa, 0.86±0.46MPa, and 1.71±0.51MPa; the average for the 200μm stromal depth was 0.08±0.06MPa, 0.08±0.04MPa, 0.08±0.04MPa, and 0.06±0.01MPa. Corneas crosslinked with the Dresden protocol and genipin were significantly stiffer than controls (p<0.05) in the anterior region only. For the control, Dresden, Accelerated, and Genipin groups, respectively, the average calculated apparent viscosity for the anterior stroma was 88.2±43.7kPa-s, 8.3±7.1kPa-s, 8.1±2.3kPa-s, and 9.5±3.8kPa-s; the average for the 200μm stromal depth was 35.0±3.7kPa-s, 49.6±35.1kPa-s, 42.4±17.6kPa-s, and 41.8±37.6kPa-s. All crosslinking protocols resulted in a decrease in viscosity in the anterior region only (p<0.05). The effects of cross-linking seem to be limited to the anterior corneal stroma and do not extend to the deeper stromal region. Additionally, the Dresden and genipin protocols seem to produce a stiffer anterior corneal stroma when compared to the accelerated protocol.