A five-food item food frequency questionnaire (FFQ) and a 3-day food diary (3DFD) were used to estimate daily dietary calcium (Ca) intake in 32 patients aged 1–17 years. Median and IQR of Ca intake from 3DFD was 840 mg and 438 mg while from FFQ it was 700 mg and 987 mg, respectively. The non-parametrical Bland-Altman limits of agreement plot between two methods showed that most of the values fell between the limits of agreement at +794 mg and −388 mg. The FFQ had a specificity of 93% in identifying children who consumed inadequate amount of dietary Ca and a sensitivity of 78% in identifying children whose dietary Ca intake exceeded UK's Reference Nutrient Intake. Thus the FFQ allows rapid estimation of children with low daily dietary Ca intake in the clinic setting; however it does not replace 3DFD.