Background: Cyst infection is a frequent and serious complication of autosomal dominant polycystic kidney disease (ADPKD) that is often difficult to treat. However, the factors influencing cyst infection are still unknown. Therefore, we investigated clinical factors related to the duration of hospitalization and death due to cyst infection. Methods: All ADPKD patients undergoing cyst drainage or nephrectomy or partial hepatectomy at Toranomon Hospital from January 2004 to March 2016, in whom cyst fluid analysis showed bacteria or neutrophils indicating definite cyst infection, were reviewed retrospectively. Factors influencing the duration of hospitalization and death due to cyst infection were analyzed. Results: A total of 243 patients with cyst infection were enrolled, including 104 men and 139 women (mean age: 62.6 ± 10.0 years). Seventeen patients died of cyst infection. Multivariate logistic regression analysis revealed that hepatomegaly, positive cyst contents culture, and the maximum white blood cell (WBC) count were significantly associated with death from cyst infection. Death was significantly more likely if patients had massive hepatomegaly (≥5,113.2 mL) compared with mild hepatomegaly (< 1,898.7 mL; odds ratio 38.1; 95% CI 2.9–492.6, p = 0.0004). Multivariate Cox proportional hazards analysis revealed that older age, dialysis duration, hepatic transcatheter arterial embolization, maximum WBC count, and hepatomegaly were significantly associated with longer hospital stay for cyst infection, while female sex, nephrectomy, serum albumin, and serum cholinesterase were significantly associated with shorter hospital stay. Discharge alive from hospital was significantly associated with massive hepatomegaly versus mild hepatomegaly (hazard ratio 0.0072; 95% CI 0.0008–0.0659, p < 0.0001). Conclusions: Hepatomegaly was strongly associated with both death and longer hospital stay due to cyst infection.