Retinal prostheses may be used to support patients suffering from age-related macular degeneration (AMD) or retinitis pigmentosa (RP). A hermetic encapsulation of the poly(imide) (PI)-based prosthesis is important in order to prevent the leakage of water and ions into the electric circuitry embedded in the poly(imide) matrix. The deposition of amorphous aluminum oxide (by sputtering) and diamond like carbon (by pulsed laser ablation) were made for applications in retinal prostheses. The thin films obtained were characterized for composition, thickness, adhesion and smoothness by scanning electron microscopy-energy dispersive spectroscopy, atomic force microscopy, profilometry and light microscopy. Biocompatibility was tested in vivo by implanting coated specimen subretinally in the eye of Yucatan pigs. While amorphous aluminum oxide is more readily deposited with sufficient adhesion quality, superior biocompatibility behavior was shown by diamond-like carbon. Amorphous aluminum oxide had more adverse effects and caused more severe damage to the retinal tissue.