Ethnic differences in the pattern and trend of growth and weight have been described in studies of migrant populations. Our objective was to compare anthropometric parameters and overweight prevalence in third and fourth generation Japanese descendant preschoolers within the Peruvian preschool population. A total of 337 measurements of height and weight from 284 children, three to five years of age, were taken over three years in one Japanese-Peruvian preschool center in Lima, Peru. The data of each parameter were classified into three ethnic groups according to their parents' surnames: Japanese descendant children (n = 104), with both parents with Japanese surnames; Japanese-Peruvian descendant (n = 93), one parent with a Japanese surname and one with a non-Japanese surname; and Peruvian descendant (n = 140), both parents with non-Japanese surnames. We used the National Center for Health Statistics (NCHS) 2000 growth charts as reference values to obtain centiles, Z scores, and body mass index (BMI). In boys, the three groups differed significantly in height, weight, BMI, Z scores, and overweight prevalence. Peruvian descendant boys were taller and heavier than Japanese-Peruvian and Japanese descendants. Moreover, Japanese-Peruvian descendant boys were taller and heavier than Japanese descendant boys. In girls, there were no significant differences in height and weight and in overweight prevalence among the three ethnic groups. Japanese descendants in Peru have height, weight and BMI values similar to those of Japanese children in Japan but lesser than Peruvian children. These findings may be related to differences in ethnic background.