Gut microbiota (GM) composition of vertebrates are considered to influence health parameters including immunological parameters in the host but knowledge of these issues in fish are sparse. We have performed a 45 day experimental study elucidating effects of dietary supplementation of organic acids (Mera Cid) and immunostimulants on the GM composition of rainbow trout Oncorhynchus mykiss (Walbaum) and investigated its association with blood parameters and disease resistance (against enteric red mouth disease (ERM) caused the bacterium Yersinia ruckeri). A total of 640 fish received either 1) basic fish feed without organic acids or immunostimulants, 2) fish feed with immunostimulants (β6glucans, MOS, nucleotides, lactic acid bacteria, vitamin C and E) but no organic acids, 3) fish feed with immunostimulants and organic acids and 4) fish feed without immunostimulants but with organic acids. Ha lf of the fish (16 groups) were then Y. ruckeri challenged on day 21 and 28 of feeding. Haemoglobin, lysozyme and gut microbiota composition (16S rRNA gene based denaturing gradient gel electrophoresis DGGE) were determined at days 14, 30 and 45. Gut microbiota analyses showed that challenge of fish with Y. ruckeri and feeding with Mera Cid affected the intestinal content.