This paper deals with the estimation of intrinsic and extrinsic parameters in a fundus camera system. These parameters are fundamental to retrieve three-dimensional reconstruction of eye's structure, in our case, retinal blood vessels. In this paper we used the Zhang's algorithm to estimate the intrinsic parameters of the optical system. Besides, an alternative method to estimate the extrinsic parameters is proposed based on the kinect one sensor. These modifications provide an easy way to characterise the whole fundus camera system. Experimental validation was carried out to verify the accuracy of the proposed method. A cylindrical known object was reconstructed having and average error of 3.96%. A real eye's structure was also reconstructed from a fundus image pair.