Background: Infections related to catheters in the upper urinary tract (CUUT) are associated with specific characteristics. Methods: A prospective observational study was carried out from 2012 to 2015 to evaluate infections in patients with CUUT. Results: A total of 209 infections were included (99 with double-J, 81 with nephrostomy, and 29 with internal/external nephroureteral stents). Among nephrostomy tube carriers, the most frequently isolated microorganisms were Pseudomonas and Enterococcus. In those with an internal/external nephroureteral stent, Klebsiella was the most common, and 57.1% were extended-spectrum beta-lactamase-producing Klebsiella. In double-J carriers, Escherichia coli and Enterococcus were the most common microorganisms. Multiple-drug resistance (MDR) microorganisms were isolated in 28.6, 47.1, and 58.3% of patients with double-J, nephrostomy, and internal-external nephroureteral stents. A percutaneous CUUT (p = 0.005) and immunosuppression (p = 0.034) were risk factors for MDR microorganisms. Conclusions: Non-E. coli bacteria are commonly isolated in patients with CUUT. MDR microorganisms are frequent, mainly in percutaneous approach or immunosuppression.