Here we describe the neurodevelopmental outcomes of very low birth weight (VLBW) infants (birth weight ≤1500 g) at 3 years of age in the Neonatal Research Network of Japan (NRNJ) database in the past decade and review the methodological issues identified in follow-up studies. The follow-up protocol for children at 3 years of chronological age in the NRNJ consists of physical and comprehensive neurodevelopmental assessments in each participating center. Neurodevelopmental impairment (NDI) – moderate to severe neurological disability – is defined as cerebral palsy (CP) with a Gross Motor Function Classification System score ≥2, visual impairment such as uni- or bilateral blindness, hearing impairment requiring hearing amplification, or cognitive impairment with a developmental quotient (DQ) of Kyoto Scale of Psychological Development score <70 or judgment as delayed by pediatricians. We used death or NDI as an unfavorable outcome in all study subjects and NDI in survivors using number of assessed infants as the denominator. Follow-up data were collected from 49% of survivors in the database. Infants with follow-up data had lower birth weights and were of younger gestational age than those without follow-up data. Mortality rates of 40728 VLBW infants born between 2003 and 2012 were 8.2% before discharge and 0.7% after discharge. The impairment rates in the assessed infants were 7.1% for CP, 1.8% for blindness, 0.9% for hearing impairment, 15.9% for a DQ <70, and 19.1% for NDI. The mortality or NDI rate in all study subjects, including infants without follow-up data, was 17.4%, while that in the subjects with outcome data was 32.5%. The NRNJ follow-up study results suggested that children born with a VLBW remained at high risk of NDI in early childhood. It is important to establish a network follow-up protocol and complete assessments with fewer dropouts to enable clarification of the outcomes of registered infants.