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The extent of the digestive/absorptive involvement in atypical presentation of celiac disease (CD) is not always clear. The aim of the study was to assess nutritional status of iron (Fe), copper (Cu), and zinc (Zn) in patients with typical CD (TCD) and atypical CD (ACD).A cross-sectional study was done in patients with TCD, ACD, and healthy controls (HC). Hemoglobin, serum ferritin, free erythrocyte protoporphyrin, Fe, Cu, ceruloplasmin, Zn, anti-endomysial antibodies, and anti-tissue transglutaminase antibodies were measured. Data were analyzed by Kruskal-Wallis, principal component analysis, and linear discriminant analysis.One hundred nine individuals were studied (54 TCD, 19 ACD, 36 HC); mean age ± standard deviation was 23 ± 15.8 (range 1.6–75.4) years. Median and range of hemoglobin were 12.8 g/dL (8.1–17.6) in TCD, 12.4 g/dL (10.5–14.5) in ACD, and 13.6 g/dL (11.1–16.7) in HC (P < 0.0001); serum ferritin was 17.7 μg/L (2.9–157), 10.8 μg/L (2.7–39.8), and 28.7 μg/L (4.5–127.2), respectively (P < 0.01). Cu was 105 μg/dL (60–185), 97.5 μg/dL (40–130), and 125 μg/dL (80–205), respectively (P < 0.05). Ceruloplasmin was 21.6 mg/dL (14.2–73.2), 22.6 mg/dL (0.9–34.3), and 32.1 mg/dL (5.8–72.6), respectively (P < 0.01). There were no differences in Fe, free erythrocyte protoporphyrin, and Zn. Principal component analysis showed that 58% of observed variability was explained by Fe and Cu indicators. Linear discriminant analysis revealed differences between CD and HC (P < 0.0001), with high values of correct classification for TCD (73%) and HC (72%), but not ACD (16%), which were mostly classified as TCD (79%).Deficiency of micronutrients was found both in typical as well as in atypical cases.