The objective of this study was to analyze the use of lumbar punctures (LP) in the evaluation of late-onset neonatal sepsis. It is recommended to perform an LP as part of the evaluation of late-onset sepsis. We used a cohort of 414 newborns with a birth weight <2000g in three hospitals in Lima. A LP was performed in 45/214 (21.0%) of sepsis evaluations and in 13/48 (27.1%) of culture-proven sepsis. Meningitis was diagnosed in 8/214 (3.7%) of the episodes and 8/45 (17.5%) of the evaluations that included an LP. The duration of treatment of the sepsis episodes without a LP and the episodes with a negative LP was similar, and shorter than the episodes with a positive LP. The use of LP in the evaluation of late-onset sepsis is low and can result in undiagnosed and undertreated meningitis. The use of LP in the evaluation of neonatal sepsis must be encouraged in the neonatal units.