Introduction and Objectives Bronchiectasis is a dilation of the peripheral airways with subsequent mucus hypersecretion. Bronchiectasis can be either genetic, that is cystic fibrosis (CF) or described as non-CF bronchiectasis (eg, idiopathic or post infectious bronchiectasis). Recently, many studies have demonstrated polymicrobial bacterial communities are present in the lower respiratory tract (LRT) of cystic fibrosis (CF) sufferers. These studies have identified complex microbial communities that are affected by many factors including age; CFTR genotype and antibiotic therapy. One prior abstract noted greater diversity in non-CF bronchiectasis as compared to CF (Bilton et al, 2009) though the sample size was small. Our aim is to extend prior work by comparing the metabolically active bacterial and fungal communities present in sputum samples from CF patients with those from non-CF bronchiectasis. Methods Adult CF and non-CF bronchiectasis patients provided spontaneously expectorated sputum samples which were treated with RNAlater. RNA was extracted from sputum samples and reverse transcribed to cDNA; this was the template for bacterial and fungal community PCR amplification using universal 16S or 28S primer sets. Amplicons were analysed by denaturing gradient gel electrophoresis (DGGE) which separates double stranded DNA based upon bacterial and fungal genomic GC content sequence. Common pathogens were identified such as Pseudomonas aeruginosa and Haemophilus spp. by comparison to a 16S or 28S standard ladder from pure cultures. Results We have compared CF and non-CF bronchiectasis (n=36 combined). Polymicrobial communities were observed in all CF and non-CF bronchiectasis patients. However, CF patients demonstrated a greater bacterial diversity with a mean of 14.77 species per sample (range 6–21) than non-CF bronchiectasis patients who had a mean of 9.67 species per sample (range 4–14). However, fungal communities were similar between CF and non-CF bronchiectasis with 73.3% and 75% of patients harbouring fungi in their LRT respectively. Similarly, CF patients had a mean of 1.33 fungal species per sample (range 0–4) whilst non-CF bronchiectasis patients had a mean of 1.16 fungal species per sample (range 0–3). Conclusions We note a complex microbiota in the lungs of both CF and non-CF bronchiectasis patients. In contrast to other studies using DNA based molecular analysis we note an increased microbial diversity observed in the CF cohort. The increases in bacterial taxa in CF may be due to differences in CFTR status, disease duration, or the intensive antibiotic regimens creating differing biological niches in non-CF bronchiectasis.