The effect of W92/72 transgenic flax seeds taken from a variety of Linola on the production of SCFA, ammonia and methane by bacteria inhabiting rabbit caecum was studied. The in vitro method was used where caecal contents from rabbits was incubated with W92/72 transgenic or Linola flax seeds, or without any additives (control samples). The total concentration of SCFA was higher in samples with the addition of flax seeds than in the control samples. The increase in concentrations of acetic, propionic and butyric acids was the highest in samples with Linola seeds added. A higher percentage of propionic and butyric acids was observed in the contents incubated with addition of flax seeds as compared to the control samples. This increase was the result of a percentage decrease in acetic acid. No differences were observed in the concentration of ammonia between fermented samples. Moreover, the addition of flax seeds resulted in slight decrease of pH in incubated samples. In gas samples, the methane level was higher in samples with flax seeds added, although the highest level was found in samples with transgenic seeds. In addition, gas pressure was significantly higher in samples with flax seeds added as compared to control samples, and this may indicate a higher intensity of microbiological fermentation processes. These studies suggest that neither Linola nor W92/72 flax seeds have any unfavorable effect on the caecal microflora activity of rabbits. A beneficial influence of flax seeds on the microbiological fermentation process in rabbit caecum was observed, based on an increase in percentage ratio of propionic acid in samples with flax seeds added.