Historically, the anthropometric assessment of nutritional welfare programs has been targeted to assess nutritional deficiencies based on weight-to-age and height-to-age indicators. Recently, given the increase on childhood obesity, it has been also recommended the measurement of indicators of obesity (i.e. weight-to-height) and central obesity (i.e. waist circumference). However, the agreement of these indicators in preschool children is unclear. The aims of this study were: 1) assess the nutritional status of children attending the Chilean National Nursery Schools Council Program (JUNJI); 2) assess the agreement between general and central obesity anthropometric measurements in these children. In 574 girls and 580 boys, 3.0 to 5.9 years old, we measured: weight, height, waist and hip circumference, and five skinfolds. We used the WHO 2006 growth standards to estimate Z-scores. We defined general obesity as WHZ or BAZ= 2, and central obesity as waist circumference >= 90 percentile of NHANES III. The participants were on average slightly shorter but considerably heavier and obese than the reference populations. Prevalence of general obesity was close to 16% with both indicators while prevalence of central obesity reached 15%. There was good agreement among general obesity indicators and central obesity indicators (Kappa = 0.6-0.7). In summary, we found a high prevalence of obesity and central obesity among Chilean preschool children beneficiaries of a welfare program. At this age, there was a good agreement among general obesity indicators and central obesity indicators. These results suggest that waist circumferences measurements should not be incorporated to the program.