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A 1‐year‐old male neutered Portuguese Podengo dog was presented for lameness, inappetence, pyrexia, diarrhoea and abdominal moderate to severe lymphadenomegaly. Cytology of synovial fluid revealed neutrophilic inflammation in multiple joints suggestive of immune‐mediated polyarthritis. Cytology of fine‐needle‐aspiration material obtained from lymph nodes revealed macrophages with intracytoplasmic, rod‐like Ziehl‐Neelsen positive staining structures, indicative of mycobacteria. Four‐month treatment with enrofloxacin, rifampicin and clarithromycin resulted in clinical improvement and resolution of polyarthritis as evidenced on repeat synoviocentesis, but diarrhoea recurred, Ziehl‐Neelsen positive organisms were again found on lymph node cytology and analysis of the 16S rRNA‐gene using the Basic Local Alignment Search Tool facility resulted in a match to Mycobacterium avium with 100% sequence identity. Treatment was adjusted to include pradofloxacin, doxycycline, rifampicin and ethambutol and 3 months later the dog is clinically normal. Based on the literature search, this is the first time canine Mycobacterium avium infection associated with immune‐mediated polyarthritis is reported. Based on scoping searches, this is the first report of canine Mycobacterium avium infection associated with immune‐mediated polyarthritis. [ABSTRACT FROM AUTHOR]