In the Neonatal Intensive Care Unit (NICU), infants' vital signs are monitored on a continuous basis via wired devices. These often interfere with patient care and pose increased risks of skin damage, infection, and tangling around the body. Recently, a wireless system for neonatal monitoring called ANNEⓇ One (Sibel Health, Chicago, USA) was developed. We designed an ongoing study to evaluate the feasibility, reliability and accuracy, of using this system in the NICU. Vital signals were simultaneously acquired by using the standard, wired clinical monitor and the ANNEⓇ device. Data from 10 NICU infants were recorded for 8 hours per day during 4 consecutive days. Initial analysis of the heart rate (HR) data revealed four problems in comparing the signals: 1) gaps in the signals - periods of time for which data were unavailable, 2) wired and wireless signals were sampled at different rates, 3) a delay between the sampled values of wired and wireless signals, and 4) this delay increased with time. To address these problems, we developed a pre-processing algorithm that interpolated samples in short gaps, resampled the signals to an equal rate, estimated the delay and drift rate between corresponding signals, and aligned the signals. Applications of the pre-processing algorithm to 40 recordings demonstrated that it was very effective. A strong agreement between wireless and wired HR signals was seen, with an average correlation of 0.95±0.04, a slope of 1.00, and a variance accounted for 89.56±7.62%. Bland-Altman analysis showed a low bias across the ensemble, with an average difference of 0.11 (95% confidence interval of -0.02 to 0.24) bpm.Clinical relevance- This algorithm provides the means for a detailed comparison of wired and wireless monitors in the NICU.