ObjectivesMicronutrient deficiencies characterize classical “late‐diagnosed” celiac disease (CeD). This study aimed to identify the prevalence of micronutrient deficiencies among children with “early‐diagnosed” screening‐identified CeD to determine the clinical value of routine testing for deficiencies in those patients.MethodsA case‐control study was conducted on screening‐identified CeD patients diagnosed during a mass screening study (84 patients, mean age 11.3 ± 2.6 years). The controls (443 children, mean age 10.8 ± 2.5 years) were negative for celiac disease serological screening. Hemoglobin, serum levels of iron, ferritin, folate, vitamin B12, vitamin A, vitamin E, 25‐OH vitamin D, zinc, and selenium were measured.ResultsThe mean serum levels of hemoglobin, iron, ferritin, vitamin D, zinc, copper, and selenium were significantly lower in CeD patients than in healthy controls (hemoglobin 12.56 vs. 13.02 g/dL [p = 0.04]; iron 10.61 vs. 17.6 µmol/L [p < 0.001], ferritin 25.7 vs. 48.3 µg/L [p < 0.001], vitamin D 29.1 vs. 37.5 nmol/L, zinc 11.9 vs. 21.7 µmol/L, copper 18.9 vs. 32.5 µmol/L, selenium 1.04 vs. 1.36 µmol/L; p < 0.001). Patients with celiac and severe intestinal damage (Marsh IIIb and IIIc) had significantly lower serum ferritin and vitamin A levels than patients with mild intestinal damage (Marsh II and IIIa) (ferritin 15 vs. 22 µg/L, p < 0.025; vitamin A 0.85 vs. 1.35 µmol/L, p = 0.007).ConclusionMicronutrient deficiencies are still detectable in “early‐diagnosed” screening‐identified CeD cases, a clinically relevant result that strongly supports efforts for screening and early diagnosis of CeD.