Abstract Objective To investigate intestinal injury, repair and vasculitis biomarkers that may illuminate the progression and/or pathogenesis of feline infectious peritonitis (FIP) or feline enteric coronavirus (FECV) infection. Materials and methods A total of 40 cats with effusive FIP (30 with abdominal effusion, AE group; 10 with thoracic effusion, TE group) and 10 asymptomatic but FECV positive cats (FECV group), all were confirmed by reverse transcription polymerase chain reaction either in faeces or effusion samples. Physical examinations and effusion tests were performed. Trefoil factor‐3 (TFF‐3), intestinal alkaline phosphatase (IAP), intestinal fatty acid binding protein (I‐FABP), myeloperoxidase‐anti‐neutrophilic cytoplasmic antibody (MPO‐ANCA) and proteinase 3‐ANCA (PR3‐ANCA) concentrations were measured both in serum and effusion samples. Results Rectal temperature and respiratory rate were highest in the TE group ( p < 0.000). Effusion white blood cell count was higher in the AE group than TE group ( p < 0.042). Serum TFF‐3, IAP and I‐FABP concentrations were higher in cats with effusive FIP than the cats with FECV ( p < 0.05). Compared with the AE group, TE group had lower effusion MPO‐ANCA ( p < 0.036), higher IAP ( p < 0.050) and higher TFF‐3 ( p < 0.016) concentrations. Clinical significance Markers of intestinal and epithelial surface injury were higher in cats with effusive FIP than those with FECV. Compared to cats with abdominal effusions, markers of apoptosis inhibition and immunostimulation to the injured epithelium were more potent in cats with thoracic effusion, suggesting the possibility of a poorer prognosis or more advanced disease in these patients.