The effects of wet (canned) or dry (kibbled) diets on faecal bacterial populations in the cat were investigated in eight domestic short-haired cats (four males and four females; averaging 6 years of age and 3·4 kg) in a nested design. The cats were fed ad libitum a commercially available wet diet (moisture 82·0 %, crude protein 51·7 %, fat 28·9 %, carbohydrate (CHO) 8·9 % and ash 10·6 % DM) for 5 weeks. On the fifth week, individual feed intakes and faecal outputs were determined. Fresh faecal samples were collected twice daily, mixed for homogeneity, subsampled and stored at − 85°C until analysis. The cats were then switched to a commercially available dry diet (moisture 8·5 %, crude protein 33·0 %, fat 11·0 %, CHO 49·4 % and ash 6·6 % DM) for 5 weeks, and fresh faeces were sampled as described previously. Energy intake tended to be higher in cats fed dry diets (P < 0·10), but body weight was similar between the two feeding periods (P>0·05). Denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rRNA genes amplified from DNA extracted from faeces was performed. The unweighted pair group method with arithmetic mean cluster analysis of bacterial community profiles using Pearson's correlation revealed diet-specific clustering when the same cats were fed on either a dry or a wet diet (dissimilarity between the groups, 88·6 %; P < 0·001). Subsequent cloning and sequencing of five selected distinct DGGE bands indicated that members of the Pelomonas and Fusobacteriaceae were influenced by a short-term change in diet format. This suggests that 5-week dietary exposure is sufficient to alter gastrointestinal microflora.