The beneficial effects of novel peritoneal dialysis solutions low in glucose degradation products regarding peritoneal cell apoptosis and necrosis are well established in vitro, however in vivo data is lacking. Cell-free DNA quantification is a possible method to determine cell damage through apoptosis and necrosis in vivo. We performed a prospective, cross-over study on 26 stable continuous ambulatory peritoneal dialysis (CAPD) patients, treating each patient for 3 months in a randomized order with a conventional, lactate-buffered, acidic solution (solution D) and a novel, bicarbonate/lactate-buffered neutral solution (solution P). The timed overnight peritoneal effluent was sampled for cell-free DNA quantification using a fluorometric assay. The effluent samples of eighteen patients were finally available for DNA quantification. The concentration range of cell-free DNA in the peritoneal effluents was 1.8–9.5 µg/L. The coefficient of intrapatient variation in overnight effluent cell-free DNA appearance was 15.6 ± 12.4%. Cell-free DNA peritoneal appearance using solutions D and P was 14.9 ± 6.8 µg and 11.8 ± 3.4 µg, respectively (P = 0.02), with the average difference of 3.1 µg (95% CI, 0.7–5.6 µg). Our results show that cell-free DNA is present in the overnight peritoneal effluent of stable CAPD patients. A significant decrease in the cell-free DNA appearance with solution P was found; however, before accepting this as an indicator of a more biocompatible profile causing less peritoneal membrane cell necrosis and apoptosis, confirmatory data on larger patient samples are needed. Our results indicate the potential future role of cell-free DNA in the diagnosis and prognosis of therapy-related peritoneal membrane degeneration.