Fibropapillomatosis (FP) is a neoplastic disease that affects marine turtles worldwide, especially green sea turtles (Chelonia mydas). FP tumors can develop on the body surface of marine turtles and also internally in the oral cavity and viscera. Depending on their quantity, size and anatomical distribution, these tumors can interfere with hydrodynamics and the ability to feed, hence scoring systems have been proposed in an attempt to quantify the clinical manifestation of FP. In order to establish a new scoring system adapted to geographic regions, we examined 214 juvenile green sea turtles with FP caught or rescued at Brazilian feeding areas, counted their 7466 tumors and classified them in relation to their size and anatomical distribution. The patterns in quantity, size and distribution of tumors revealed interesting aspects in the clinical manifestation of FP in specimens studied in Brazil, and that FP scoring systems developed for other areas might not perform adequately when applied to sea turtles on the Southwest Atlantic Ocean. We therefore propose a novel method to evaluate the clinical manifestation of FP: fibropapillomatosis index (FPI) that provides the Southwest Atlantic fibropapillomatosis score (FPSSWA). In combination, these indexing and scoring systems allow for a more objective, rapid and detailed evaluation of the severity of FP in green sea turtles. While primarily designed for the clinical manifestation of FP currently witnessed in our dataset, this index and the score system can be adapted for other areas and compare the characteristics of the disease across regions. In conclusion, scoring systems to classify the severity of FP can assist our understanding on the environmental factors that modulate its development and its impacts on the individual and population health of green sea turtles.