Conjunctivitis associated systemic lupus erythematosus (caSLE) is a connective tissue autoimmune disease with a large spectrum of clinical manifestations. The disease may lead to ocular complications and in severe cases may be sight-threatening. This study investigated the expression of vascular adhesion protein-1 (VAP-1) in SLE patients with conjunctivitis and the relationship between VAP-1 and other proteins in the onset of the disease. Ten patients with caSLE (caSLE group) and 10 healthy volunteers (control group) were enrolled in the study, in order to evaluate the VAP-1 expression levels in blood. Protein expression profiling was performed with two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and analyzed with matrix-assisted laser desorption/deionization time-of-flight (MALDI-TOF) used in tandem with mass spectrometry. In the caSLE group, 8 proteins were expressed differenty compared with the control group: C-reactive protein, hemoglobin subunit β, VAP-1, A-albumin (AFAM), enolase and immunoglobulin heavy constant mu were upregulated; interferon regulatory factor-1 and serum amyloid A2 protein were downregulated. Western blotting results are consistent with the proteomics results, showing that in caSLE group VAP-1 expression is increased in comparison to the control group. VAP-1 protein participates in the inflammatory reaction in the form of amine oxidase, copper containing 3. Bioinformatics analysis suggested that VAP-1 protein could be used as a candidate protein for further study regarding its role as a potential protein marker for screening and effectively monitoring caSLE.