The objective of the study was to determine the differences in systemic stress response in patients undergoing transurethral resection of the prostate (TURP) versus endoscopic laser ablation of the prostate (ELAP) for benign prostatic hyperplasia (BPH). The study included 48 patients with BPH (24 treated by TURP and 24 by ELAP). Blood samples were taken from each patient before and immediately after the procedure and on postoperative days 1, 6, and 20, respectively. TURP caused more intense acute-phase response during 24 h after the procedure considering the serum c-reactive protein (CRP) level (p < 0,001) and absolute leukocyte (p = 0.001) and neutrophil number (p = 0.003) in peripheral blood. ELAP caused more decrease in the number of natural killer cells immediately after the procedure (p = 0.048). There were no statistically significant differences between TURP and ELAP procedures in protein and creatine kinase (CK) levels, adrenocorticotropic hormone, and cortisol as well as other immunological parameters. TURP causes more intense acute-phase response than ELAP.