In this article we present a new method to estimate precisely the cross-section of tubular organs. Obtaining a precise cross-section is the critical step to perform quantitative analysis of those organs, for which diameter or area are often correlated to pathologies. Our estimation method, based on a covariance measure from the Voronoi cells of the set of studied points, can be computed either from the skeleton representation, or from the whole set of voxels of the segmented tubular organ. This estimator can give a cross-section estimation from any point of the organ, and is both more accurate and more robust to segmentation errors than state-of-the-art methods.