Fluroquinolone prophylaxis during haematopoietic cell transplantation (HCT) remains controversial. We aimed to determine the effect of ciprofloxacin prophylaxis on the incidence of infections and the impact on the immune system. The study found that ciprofloxacin prophylaxis did not significantly reduce the incidence of infections, but it did have a significant impact on the immune system, leading to changes in the gut microbiome and an increased risk of antibiotic resistance. The findings of this study have important implications for the use of ciprofloxacin prophylaxis in HCT and highlight the need for further research into the optimal use of antibiotics in this setting.