Simple SummaryParatuberculosis (PTB) is a well-known disease with considerable financial impact on the farm industry worldwide. Nevertheless, data regarding the assessment of naturally infected goat herds is limited. The present study describes in detail the observed gross and histological lesions detected in 39 necropsies of goats (15 vaccinated and 24 non-vaccinated) from herds with a confirmed history of PTB. PTB microscopic lesions of various grades were detected in all animals in target organs and the presence of the causative agent was confirmed using different laboratory tools. The main inflammatory findings affected the hemolymphatic, respiratory and gastrointestinal systems. The lesions were confirmed microscopically with lesser macroscopically visible alterations. Our result demonstrated that non-vaccinated animals presented more severe PTB intestinal lesions and had respiratory inflammation in all age groups studied. Those also presented a higher prevalence of ileocecal valve PTB lesions. Gastrointestinal non-PTB lesions were detected in higher number in non-vaccinated goats. Thus, histology is a powerful tool for herd diagnosis and assessment. Mainly inflammatory lesions of the respiratory and gastrointestinal tract were detected in the studied PTB-affected herds. Additionally, vaccination against PTB could play a key role in the reduction of lung and gastrointestinal inflammatory processes present in the herd.AbstractParatuberculosis (PTB), caused byMycobacterium aviumsubspeciesparatuberculosis(MAP), causes significant financial losses in the ruminant industry. The aim of this study is to describe the concomitant pathological findings as well as PTB-induced lesions in 39 naturally infected goats (15 vaccinated and 24 non-vaccinated). All animals exhibited MAP-induced microscopic lesions affecting target organs, although only 62% of those were detected grossly. Mainly concomitant inflammatory pathologies were recognized affecting the hemolymphatic, respiratory and gastrointestinal systems. Non-vaccinated animals exhibited both moderate and marked granulomatous enteritis in contrast with vaccinated ones which presented mild intestinal affection. Our results demonstrate that non-vaccinated animals presented pneumonia in all age groups studied (from 12 up to >48 months old). A significantly higher prevalence of ileocecal valve PTB lesions was detected in non-vaccinated animals with pneumonic lesions (p= 0.027). Furthermore, a reduction of gastrointestinal non-PTB processes was described in vaccinated goats. In conclusion, a PTB infected goat herd can be affected by a wide range of concomitant pathologies, mostly inflammatory in origin. Anatomic pathology is of crucial importance for correct herd diagnosis and histopathology is an indispensable tool for lesion detection. Additionally, anti-MAP vaccination could have a beneficial effect on the reduction of respiratory and gastrointestinal non-PTB diseases.