Paraquat (1,1'-dimethyl-4,4'-bipyridinium chloride, PQ) is a non-selective herbicide, and PQ poisoning by accidental or intentional ingestion is a cause of numerous fatalities around the world every year. Although a great deal of research has been conducted into the development of an acceptable treatment for PQ poisoning, no effective guidelines for patients have been developed thus far. Acai berry extract and juice have been highlighted in this regard, due to their observed antioxidant effects in various diseases. Furthermore, the acai berry has been used in dietary supplements, as it contains a variety of nutrients, including proteins, lipids, vitamins A, C and E and polyphenols. In this study, we conducted proteomic analysis of PQ-poisoned rat lungs to evaluate the changes in protein expression induced by PQ and to identify any protective effects of acai berry on the PQ poisoning. Our data revealed that the expression of the calcium signaling-related proteins calcium binding protein 1 (CaBP1), FK506 binding protein 4 (FKBP4), S100A6 and secreted protein acidic and rich in cysteine (Sparc, also known as osteonectin) were induced by PQ treatment and downregulated by acai berry treatment. However, the levels of protein kinase C substrate 80K-H were shown to be downregulated as the result of PQ treatment. Our results indicated that these proteins may function as biomarkers for acute poisoning by PQ exposure. Further studies may be necessary to understand their clinical relevance with regard to PQ poisoning.