Background <p>In Hematopoietic Stem Cell Transplantation (HSCT) recipients, Lower Respiratory Tract Infection (LRTI) is a leading cause of Intensive Care Units (ICU) admission and mortality. Although Cytomegalovirus (CMV) reactivation is a known risk factor for worse outcomes in HSCT recipients, the specific prognostic impact of CMV DNAemia on critically ill HSCT recipients with LRTI is not well-defined. This study aimed to determine the relationship between plasma CMV DNA levels at ICU admission and mortality in this high-risk population.</p> Methods <p>This retrospective study collected adult patients who have admitted to a single-center ICU received HSCT and were diagnosed with LRTI. Based on plasma CMV DNA levels tested within 48&#xa0;h of admission, patients were grouped as CMV positive (&gt; 10³ copies/mL) or CMV negative (≤ 10³ copies/mL). We performed a 1:1 propensity score matching to control for confounding factors. The primary outcome was ICU mortality. Secondary outcomes including 1-year mortality, ventilator-free days, and ICU length of stay. Survival of CMV positive or negative patients was examined with Cox regression.</p> Results <p>From 606 eligible patients, each of 155 patients were matched for the two groups by propensity score matching. The CMV positive group exhibited a significantly higher ICU mortality rate compared to the CMV negative group (32.35% vs. 25.80%, <i>P</i> = 0.011). A Cox regression analysis, adjusted for age, WBC count, SOFA score, PaO₂/FiO₂, and GvHD, confirmed that CMV positivity was independently associated with a higher risk of 1-year mortality (HR = 1.27, 95% CI [1.10–2.33], <i>P</i> = 0.002). The ventilator-free days and ICU length of stay did not significantly differ between the two groups.</p> Conclusion <p>In HSCT recipients admitted to the ICU with LRTI, CMV DNAemia at admission is an independent predictor of both short-term and long-term mortality.</p>