Eggshell morphology is a valuable indicator of the local conditions within the nests of modern crocodilians and birds. In contrast to these latter, the anatomical structure of the eggshells of most crocodilian species is practically unknown. Here, we provide the first characterization of crocodilian eggshells, using x-ray micro-CT scans. We studied eggshells of Caiman latirostris and Caiman yacare from various developmental stages that coincide with the beginning of embryonic ossification. The new 3D renderings revealed complex ornamentation, unique among crocodilians, and amphora-shaped pore canals, some of which converge in single pore openings. We also documented a high density of pore canals with a gas diffusion capacity 45 times higher than the average predicted for modern avian eggshells. The external ornamentation and the thickness of the compact layer of the eggshells (i.e. excluding ornamentation) showed ontogenetic and interspecific differences that could be related to nesting materials and nesting areas selected by each species. The shell features described here evidence a greater structural complexity than previously recognized in phylogenetically close, sympatric crocodilian species. Further comprehensive morphological analyses on other modern and fossil crocodilian eggshells using micro-CT technology will shed new light on the evolution of reproductive strategies in this intriguing archosaur clade.