Mechanical ventilation (MV) is commonly used in neonatal intensive care units (NICUs) to support breathing. Anecdotally, male infants are harder to ventilate than females. In this study, the pulmonary mechanics of 10 invasively mechanically ventilated neonates from Christchurch Women’s Hospital, recorded during an observational trial with no protocolised change to care, are compared. We hypothesise males have higher specific lung elastance (elastance corrected for weight) than females, due to stiffer and less developed lungs. The specific elastance and resistance is identified for every breath using a single compartment model with a pressure loss term added to compensate for endotracheal tube resistance. Variability is determined by relative percent breath-to-breath variability (%ΔE) in specific elastance. Male infants had higher specific elastance compared to females (P≤0.01) with median [interquartile range] of 1.91[1.33‐2.48] cmH2O.kg/ml and 1.31[0.86‐2.02] cmH2O.kg/mL respectively. Males also had lower %ΔE median IQR of -0.03 [-7.56 - 8.01] and females had 0.59[-12.56 - 12.86]. The results validates our hypothesis that boys have higher elastance than girls. These results also suggests males and females should be ventilated differently.