Background: Percutaneous nephrolithotomy (PNL) is the initial therapy of choice for stones in the kidneys that are over 2 cm in size, although the majority of patients undergoing PNL recover rapidly and discharge early, some patients still required prolonged length of hospital stay (LoS). Aim: To identify factors affecting LoS in patients undergoing PNL. Research design: Prospective (cohort) research design was utilized. Setting: At Assiut Urology University Hospital. Sample: A convenience sample of 138 adult patients who had undergone PNL surgery. Tools: Patients assessment sheet. Results: Out of 138 patients, 41 (29,7%) had prolonged LoS, The mean duration of hospital stay was (3.2±1.13) days, ( rang 1-7), multivariate logistic regression analysis reflect that the presence of diabetes mellitus (P= 0.013, OR= 2.33, 95% CI, [1.62-65.08]), high serum creatinine level (P=0.004, OR= 1.12, 95% CI [1.43-6.51]) postoperative pain (P=0.049, OR= 2.81, 95% CI [1.02-271.89]), postoperative urinary tract infection (P=0.010, OR= 1.56, 95% CI [1.46-15.37]) were identified as independent factors affecting LoS in patients undergoing PNL. Conclusion: Diabetes mellitus, high serum creatinine level, postoperative pain and postoperative urinary tract infections were identified as independent factors that prolong LoS. Recommendation: Factors that affect LoS should early be identified to reduce health care expenditures and work burden on medical staff.