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Previous studies have demonstrated that the pharmacological activities displayed by the venom of the snake Bothrops jararaca undergo a significant ontogenetic shift. Variation in the venom proteome is a well-documented phenomenon, however, variation in the venom peptidome is poorly understood. We report a comparative proteomic and peptidomic analysis of venoms from newborn and adult specimens of B. jararaca and correlate it with the evaluation of important venom features. We demonstrate that newborn and adult venoms have similar hemorrhagic activities, while the adult venom has a slightly higher lethal activity upon mice; however, the newborn venom is extremely more potent to kill chicks. The coagulant activity of newborn venom upon human plasma is ten times higher than that of adult venom. These differences were clearly reflected in their different profiles of 2D-PAGE and spot identification, gelatin zimography, immunostaining using specific antibodies, glycosylation pattern, and concanavalin A-binding proteins. The venom comparison by isobaric tag peptide labeling (iTRAQ) revealed clear differences in toxin levels. Metalloproteinases, serine proteinases and growth factors are among the proteins with higher expression in adult venom. Furthermore, we report the analysis of the peptide fraction of newborn and adult venoms by MALDI-TOF mass spectrometry and LC/MS/MS which revealed different contents of peptides, while the bradykinin potentiating peptides (BPPs) showed rather similar profiles, and were detected in the venoms showing their canonical sequences and also novel sequences corresponding to BPPs processed from their precursor protein at sites so far not described. As a result of these studies, we demonstrate a clear relationship between the ontogenetic shift in diet and animal size, and the venom proteome/peptidome in B. jararaca species.