Weights of kidneys, heart, lungs, liver, adrenals, eyes and tongue of the northern form of franciscana (Pontoporia blainvillei) and the estuarine dolphin (Sotalia guianensis) incidentally caught in fishing nets are presented and related to total body weight. Because of the smaller body size of the northern form of P. blainvillei, its actual organ weights were all smaller than those of the southern form reported in the literature. However, the lungs and adrenals of the northern form were proportionally greater than those of the southern form. The relative weight of the males' left kidney (N=18) and females' liver (N=17) were significantly heavier in this study than the proportions presented elsewhere in the literature for the southern form of the species. However, the females' kidneys, males' right kidney and males' liver did not differ between the northern and southern forms, and a larger number of individuals of both geographical forms should be analysed. The actual weights of the S. guianensis internal organs were all greater than those reported in the literature for S. fluviatilis. Additionally, the body-to-organ mass proportions of kidneys, heart and lungs of S. guianensis were also greater than those of S. fluviatilis. This study provides comparative data that can be used when examining the systematics of both species and provides a baseline for future examinations of the post-mortem conditions of these cetacean species.