A standard growth chart is indispensable for evaluating an individual’s growth. In Japan, the cross-sectional growth chart from fiscal year 2000 is most commonly used in the clinical setting. However, when using the current standard growth chart to assess growth during puberty, two problems are encountered. First, the individual pubertal height trajectory does not fit the cross-sectional growth chart because the pubertal height curve of individuals rises more sharply than that indicated by the cross-sectional growth chart. Second, variations in the timing of an individuals’ growth spurt render it difficult or impossible to assess individual growth patterns using a single chart. To address these two issues, new growth charts were established using height measurements of 6744 boys and 6929 girls born between April 1975 and March 1976 in the Akita Prefecture. Individuals whose age at peak height velocity (age^PHV) was 2 standard deviation greater or lesser than the mean were excluded, and the remaining participants were divided into three groups according to the first and third quartiles of age^PHV. Finally, we established three longitudinal growth charts each for boys and girls based on a healthy Japanese population.