Soil color originates mainly from organic matter, iron mineralogy and moisture content. We aimed to find a suitable method to measure soil color sensitively and to evaluate the extent to which the color parameters can be useful for statistically estimating total carbon (C), total nitrogen (N) and active iron (Fe) contents in Japanese agricultural soils. A soil color reader (SPAD-503) was applied to two sample sets: (1) 100 surface soils collected throughout a 0.5-ha paddy field (field scale) and (2) 147 surface soils collected from agricultural fields in Japan (national scale). For analysis with this instrument, about 2 g of air-dried, finely-ground samples were packed firmly in a plastic cell, and their colors as they appeared on windows in both sides of the cell were measured. A CIE 1976 (L*, a*, b*) color space was used for color description. For the field-scale samples, the values of the coefficient of variation were around 15% for total C, total N and acid oxalate extractable iron (Fe_o). The L* value (lightness) was negatively correlated with the content of total C and total N (R² = 0.18** and 0.26**, respectively), and the b* value (yellowness) was positively correlated with the Fe_o content (R² = 0.59**). For the national-scale samples, the values of the coefficient of variation were around 60% for total C, total N and Fe_o. The L* value was negatively correlated with the content of total C and total N (R² = 0.70** and 0.59**, respectively), but the b* value was not correlated with the content of Fe_o (R² = 0.00). When the analysis was limited to 65 samples frequently used for paddy fields, the b* value was positively correlated with the Fe_o content (R² = 0.52**). In conclusion, the proposed method enabled us to measure soil color sensitively with a small sample size. The L* and b* values obtained can be useful for rapid estimation of total C, total N and Fe_o contents in agricultural surface soils in Japan.