BackgroundThe diagnostic value of procalcitonin (PCT) for patients with autoimmune diseases (AID) remains controversial and few studies focused on ICU patients. We sought to determine its diagnostic and prognostic values in this clowd.MethodsA prospective observational study was conducted in AID patients admitted to the ICU. Serum PCT levels were measured on ICU admission and subsequently at days 1, 3, 5 and 7, and peak PCT levels within 24 h (PCTpeak) were analyzed the utility for bacterial infection. The relationship of PCTpeak and SOFA score and severity of sepsis was performed correlation analysis. The change of PCT over time reflected as PCT clearance was compared to ICU 28-day mortality.ResultsOne hundred twelve patients were divided into bacterial infection group (group I, n = 54) and nonbacterial condition group (group II, n = 58). The median PCTpeak (range, μg/L) was higher in the group I than that in the group II (1.95 [0.38–37.56] vs. 0.64 [0.05–7.83], p = 0.002). PCTpeak had the best single predictor of bacterial infection (area under the curve [AUC], 0.902, p < 0.001) with a sensitivity of 79.6 % and a specificity of 89.6 % at the threshold of 0.94 μg/L. PCTpeak was also positive correlation with severity of sepsis (r = 0.731, p = 0.002), but its correlation with SOFA score was only found in subjects with bacterial infection (r = 0.798, p < 0.001). Importantly, the 5-day PCT clearance (PCTc-d5), rather than absolute PCT values, could earlier discriminate survivors (n = 73) from nonsurvivors (n = 39) (68.8 ± 9.8 vs. 21.8 ± 17.5 %, p < 0.001, respectively). PCTc-d5 < 50 % was an independent predictor of mortality (odds ratio 5.1, 95 % confidence interval 3.5 to 7.5; p = 0.001).ConclusionsIn critically ill patients with AID, elevated PCT levels are valuable for bacterial infection and are significantly positive correlation with the septic severity. Five-day PCT clearance may provide independent prognostic information. Larger, prospective trials are warranted to confirm the benefit.Electronic supplementary materialThe online version of this article (doi:10.1186/s12871-015-0122-9) contains supplementary material, which is available to authorized users.