With this study, we provide insight into the clinical characteristics, laboratory characteristics, and organ damage associated with incomplete lupus syndromes (ILE) and search for predictors of organ damage in ILE. A retrospective chart review was performed on 77 hospitalized patients with ILE. The control patient group comprised 2104 systemic lupus erythematosus (SLE) patients who were entered into the Chinese SLE Treatment and Research group (CSTAR). The Systemic Lupus International Collaborating Clinics (SLICC)/ACR Damage Index (SDI) was used to classify damage features. Based on their SDI score, ILE patients were divided into SDI > 0 and SDI = 0 groups. The percentages of anti-SSA-seropositive (54.5 %) and anti-RNP-seropositive (24.7 %) patients with ILE were higher than those found among the SLE patients from CSTAR (p < 0.001). The mean SDI score was 0.66 (range 0-2), and a damage score greater than 0 was present in 41 (53.3 %) patients. The most prevalent damage category was pulmonary damage, present in 17 (22.1 %) patients. Peripheral vascular damage occurred in individuals who were significantly older than those who had musculoskeletal damage (p = 0.031). The subgroup with SDI > 0 had a higher mean age (36.8 ± 2.04 years) than those with SDI = 0 (30.8 ± 2.08 years; p = 0.044). The mean SLEDAI score in the SDI > 0 patient group (8.2 ± 0.74) was higher than that of the SDI = 0 group (4.8 ± 0.54; p = 0.001). ILE patients may include a subset that is likely to experience progressive organ damage. Organ damage was more common in patients of older age and with high SLEDAI scores.