Transparency is an important criterion for the application of biomaterials to the eye and essential for use as a vitreous substitute. However, there is a lack of understanding on the features of transparent hydrogels and the boundaries of transparency of various hydrogel systems. In this paper, we tune the poly[(R)-3-hydroxybutyrate-(R)-3-hydroxyhexanoate] (PHBHx) content of biodegradable PHBHx-based polyurethane thermogels and show that the amount of hydrophobic PHBHx correlates with hydrogel cloudiness. We found that PHxEP-0.5 hydrogel shows high light transmittance and suitable gel properties as a vitreous substitute. The PHxEP-0.5 hydrogel is able to maintain transparency when implanted in rabbit eyes as opposed to a cloudy gel and shows negligible inflammation and preservation of the retinal structure over 6 months. In conclusion, we show that PHBHx-based thermogels can be tuned for transparency and are biocompatible in the rabbit eye. These results could be instructive for the design of a new generation of injectable transparent vitreous substitutes.