Body masses for 14 species of pterosaur spanning four orders of magnitude were estimated using three-dimensional, digital models. The modeled taxa comprised seven paraphyletic ‘rhamphorhynchoids’: Anurognathus ammoni, Dimorphodon macronyx, Eudimorphodon ranzii, Jeholopterus ningchengensis, Preondactylus buffarinii, Rhamphorhynchus muensteri, and Sordes pilosus; and seven pterodactyloids: Anhanguera santanae, Dsungaripterus weii, Pteranodon longiceps, Pterodaustro guinazui, Pterodactylus sp., Quetzalcoatlus northropi, Tupuxuara longicristatus. The reliability of the mass estimation methods were tested with equivalent models of six extant species of bird with masses that spanned three orders of magnitude. The close agreement between model bird mass estimates and those of the living forms provides a level of confidence in the results obtained for the extinct pterosaurs. The masses of the axial body regions (tail, trunk, neck, head), limbs, and patagia of the pterosaurs were individually estimated and distinct differences in relative body proportions were found between species. Allometric relationships between body length and wingspan and body mass were derived for ‘rhamphorhynchoids’ and pterodactyloids to facilitate the estimation of body masses for other pterosaurs known from incomplete material, and these relationships also highlight differences in phyletic shape change between the two groups. The estimated mass for the largest pterosaur known, Quetzalcoatlus northropi, exceeds the previous highest estimates by more than 100%, and it is argued that this extremely large pterosaur is better interpreted as a secondarily flightless form.