The current study evaluates the indices of glucose control for diabetics (i.e., glycated albumin (GA), hemoglobin A1c (HbA1c), plasma glucose (PG) and immuno-reactive insulin (IRI)) in non-diabetic children from a population-based cohort, and compares those values according to the presence of obesity to examine any differences in these indices. GA, HbA1c, casual PG and casual IRI in obese children (n = 209) were compared to those of non-obese children (n = 1060) in Ina town, Saitama Prefecture, in 2002-2003. In obese children, the levels of HbA1c, PG and IRI were statistically higher when compared to those of non-obese children. In contrast, the median and intra-quartile range (IQR) of GA of obese children (13.6%: 12.6-14.7) was statistically lower when compared to that of non-obese children (14.3%: 13.5-15.4, p < 0.001). The low GA (%) in obese children is mainly due to the low absolute value of GA (g/dl) rather than a higher albumin value (g/dl). This is the first report to reveal that GA levels are low in obese, non-diabetic children. Additional data collection and an experimental approach are necessary to reveal the reasons behind lower GA levels in obese children.