Background and objective: In Bronchiectasis not caused by Cystic Fibrosis (BE), chronic, polymicrobial airway infection contributes to the underlying pathogenesis of disease. There is little information on whether bacterial community composition relates to clinical status. We determined the relationship between bacterial community composition, chest high resolution computed tomography (HRCT) scores and clinical markers in BE. Methods: A sub-group of BE patients from a previous cross-sectional study were analysed. Spontaneously expectorated sputum was analysed using culture-independent sequencing on the Roche 454-FLX platform covering the V1-V3 region of the 16S rRNA marker-gene. Chest HRCT scans, multiple breath washout, spirometry and blood inflammatory markers were collected. Pearson (r) correlation coefficient was used to assess relationships. Results: Data from 21 patients were analysed (mean [SD] age 64.0 [7.7]; female:male 14:7; mean [SD] FEV1 76.5 [17.2]). All bacterial community composition metrics (bacterial richness, diversity, evenness, dominance) correlated with percentage BE score, with more severe HRCT abnormality relating to lower bacterial richness, evenness and diversity (range r= -0.47 to -0.66; p<0.05). Inflammation (C-reactive protein and white cell count) was greater in patients with lower diversity and richness (range r=-0.44 to -0.47; p<0.05). Bacterial community characteristics did not correlate with lung function. Conclusion: This is the first study to indicate a relationship between bacterial community characteristics by 16S rRNA marker-gene sequencing, structural damage as determined by chest HRCT and clinical measures in BE. The association between loss of diversity and chest HRCT severity suggests bacterial dominance with pathogenic bacteria may contribute to disease pathology.