In this chapter, we focus on the effects of bacterial infections on urinary proteome. Escherichia coli and Staphylococcus aureus are two of the most common human pathogens. Three rat models were established: (i) the intraperitoneal co-injection of E. coli and S. aureus model (ES model), (ii) the intraperitoneal injection of E. coli model (E model), and (iii) the intraperitoneal injection of S. aureus model (S model). The urinary proteomes of the three models on days 0, 1, and 2 were analyzed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Compared with those on day 0, a total of 111, 34, and 94 differential proteins were identified in the ES model, E model and S model, on days 1 and 2, respectively. Approximately 47% of the differential proteins in the E model were found to overlap with those in the ES model, while 36% of the differential proteins in the S model were found to overlap with those in the ES model. Compared with the E model and S model, a total of 72 unique differential proteins were identified in the ES model. Our findings suggested that (1) the urine proteome could distinguish between different bacterial intraperitoneal injection models and (2) the effects of co-injection with two bacteria on the urine proteome were not simple a superposition of those in single injection.