The relationship between inflammatory bowel disease and microorganisms was evaluated. The presence of Candida albicans-specific IgM and IgG antibodies in serum samples and the presence of C. albicans in stool and colonal mucosa samples of the patients did not exhibit any significant difference between 21 patients in active stage and 15 patients in remission of ulcerative colitis (UC) (compared with 19 control patients). The invasion of yeast cells to the colonal mucosa was demonstrated by detecting C. albicans DNA using specific PCon1, PCon2, and PspA(2) Primers in PCR assay. Eighteen of 36 patients (50 %) were found to be DNA positive while in 19 controls only 4 (21 %) were found to be positive. The presence of DNA in the association of the positive serological reactivity is suggested as an important diagnostic marker of UC.