For diagnosis of CMV infection in colon biopsies, immunohistochemistry (IHC) and polymerase chain reaction (PCR) can be helpful besides pathologic examination. We performed CMV IHC and PCR on formalin–fixed paraffin-embedded (FFPE) and fresh tissue (FT) in clinically suspicious children for colitis and compared the results with the patients’ clinical course. In a prospective cohort study, among 153 candidate children for the colonoscopy due to colitis, 50 showed positive CMV PCR on FT. PCR on FFPE tissue was positive in 17/40 (42.5 %) cases, of which 2/40 (5%) had positive IHC. Low titer plasma CMV DNA level was seen in 7/17 FFPE-PCR positive cases. Two patients had a high plasma CMV DNA level, who were the two IHC-positive cases. Fecal calprotectin level showed an association with disease histologic activity, but not with CMV positivity on either of the methods of detection. IHC positivity was more likely to be associated with a high plasma CMV DNA level. There was a high rate of false positivity by CMV PCR test on fresh tissue that was neither associated with histopathology nor with the CMV DNA plasma level. Antiviral treatment was correlated with a poorer outcome in patients with inflammatory bowel disease (P=0.035). Conclusion: The PCR result of FT is correlated neither to histology nor to the serum CMV-DNA level. High fecal calprotectin level is associated with active lesions in histopathology. Large randomized clinical trials are recommended to assess the efficacy of antiviral treatment in acute colitis cases that have a high copy number of CMV in the blood or positive results on IHC.