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Hyperammonemia, in the absence of significant liver dysfunction, is an uncommon but often fatal occurrence following orthotopic lung transplant. Prior reports have provided evidence to support Ureaplasma species as an etiology for this syndrome. This case report describes an individual post-lung transplant, treated emperically with doxycycline along with other measures to lower ammonia levels, at the time hyperammonemia with encephalopathy was recognized. The patient clinically improved. Ureaplasma species were subsequently identified using 16S ribosomal RNA gene PCR/sequencing of pleural fluid, and by culture of bronchoalveolar (BAL) fluid. This case provides further support for empiric treatment of Ureaplasma species upon recognition of hyperammonemia syndrome post-lung transplant.