Conjugated linoleic acid (CLA) is formed from linoleic acid (LA; cis-9,cis-12-18:2) by intestinal bacteria. Different CLA isomers have different implications for human health. The aim of this study was to investigate LA metabolism and the CLA isomers formed in two individuals (V1 and V2) with different faecal metabolic characteristics, and to compare fatty acid metabolism with the microbial community composition. LA incubated with faecal samples was metabolized at similar rates with both subjects, but the products were different. LA was metabolized extensively to stearic acid (SA; 18:0) in V1, with minor accumulation of CLA and more rapid accumulation of vaccenic acid (VA; trans-11-18:1). CLA accumulation at 4 h was almost tenfold higher with V2, and little SA was formed. At least 12 different isomers of CLA were produced from LA by the colonic bacteria from the two individuals. The predominant (>75%) CLA isomer in V1 was rumenic acid (RA; cis-9,trans-11-18:2), whereas the concentrations of RA and trans-10,cis-12-18:2 were similar with V2. Propionate and butyrate proportions in short-chain fatty acids were higher in V1. A 16S rRNA clone library from V1 contained mainly Bacteroidetes (54% of clones), whereas Firmicutes (66% of clones) predominated in V2. Both samples were devoid of bacteria related to Clostridium proteoclasticum, the only gut bacterium known to metabolize VA to SA. Thus, the CLA formed in the intestine of different individuals may differ according to their resident microbiota, with possibly important implications with respect to gut health.