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We investigated the clinical effectiveness of subcutaneous (SC) administration of recombinant feline interferon-omega (rFeIFN-ω) at a dose of 1 M unit (MU)/kg body weight (bw) for the treatment of feline chronic gingivitis-stomatitis (FCGS) in cats infected with feline calicivirus (FCV). Among the 17 cats used in this study, there were 13 FCV-positive cats (FCVI group), which were subcutaneously injected with rFeIFN-ω. The remaining four FCV-positive cats (FCVC group) were treated with SC corticosteroid. SC injection of rFeIFN-ω was given once daily on days 1, 2, 3, 7, 8, 9, 14, and 21. Corticosteroid was subcutaneously injected at a dose of 1.0 mg/kg bw, at the same intervals as rFeIFN-ω. Clinical symptoms (salivation, pain at opening the mouth, halitosis, mandibular lymphadenopathy, and all four symptoms combined [defined as “total clinical symptoms”]) and stomatitis (the degree and extent of inflammation, bleeding from the lesion, and all three items combined [defined as “total stomatitis”]) were scored on days 0, 7, 14, 21, and 28. FCV RNAs was quantified by real-time polymerase chain reaction and the percent increase in viral copy numbers was calculated using the values on days 0 and 28. In the FCVI group, significant differences were observed in the score for clinical symptom (salivation) score and in the total clinical symptom score within the group (P = 0.018 and 0.008, respectively). Significant differences within the group were also observed in the scores for the degree and extent of inflammation in stomatitis and in the total stomatitis score (P = 0.003, 0.007, and 0.003, respectively). The total score, defined as the clinical score plus the stomatitis score, was on days 7, 14, 21 and 28 than on day 0 (p = 0.006, .0003, 0.002 and 0.002, respectively). In the FCVI group, significant difference was observed between on days 0 and on 21 (p = 0.023). The percentage change in the number of polymerase chain reaction cycles required to amplify the viral RNA was positive (indicating viral reduction) in the FCVI group, but was negative in the FCVC group. These results demonstrate that SC administration of rFeIFN-ω under the current protocol improves stomatitis by inhibiting FCV proliferation in FCV-positive cats with FCGS.