The aim of the study was to analyze the occurrence of anemia in children with newly diagnosed Crohn's disease and 3 months after the initiation of treatment depending on location and activity of the disease. 36 children aged from 2 to 18 years with newly diagnosed Crohn's disease treated in the years 2005-2011. According to the classification of Paris children were divided into 2 groups: II - 9 children (0-10 years); II - 27 children (11-17 years). We analyzed RBC, Hb, HCT, MCV, Fe, PCDAI at diagnosis and 3 months after the treatment, depending on the location and phenotype of the disease. Anemia was defined according to WHO criteria. Children were treated in accordance with the standards and activity of the disease. During the observation period supplementation of iron was not used. We analyzed the potential factors that could affect on the incidence of anemia. In the group I mean activity of the disease was lower than in group II in both observed periods. No statistically significant differences in hemoglobin, red blood cell count, hematocrit and volume of erythrocytes at diagnosis and after 3 months were noted. The average iron concentration increased from 6.98 microg/dl to 9.95 microg/dl (p < 0.05) after the treatment. A statistically significant higher incidence of iron deficit in group II in both analyzed periods was observed, respectively, 66.7% vs 92.59% and 55.5% vs 77.77% (p < 0.05). Anemia was more frequent in group II (p > 0.05). After 3 months of treatment the incidence of anemia reduced from 63.88% to 44.4% (p < 0.05) and iron deficit from 83.3% to 72.2% (p > 0.05). Inflammatory changes in upper gastrointestinal tract were found in 61.1% of children with Helicobacter pylori infection in 8.3% of cases. Ileal location was observed in 52.7% of children, more often in group II than I, 62.9% vs 22.22% (p < 0.05). Isolated location of inflammatory lesions in the colon more frequently observed in group I than II, respectively 55.5% vs 29.6% (p < 0.05). Thiopurine were used in 38.8% of children more often in group II than I, respectively 48.1% vs 11.1% (p < 0.05). Corticosteroids were used in 50.0% of children, often in group II than I, respectively 55.5% vs. 33.3% (p > 0.05). In children with newly diagnosed Crohn's disease anemia was diagnosed in 63.88% of the children and in 47.2% of children after 3 months of treatment (p < 0.05), iron deficiencies, respectively, in 83.3% and 72.2% of children (p > 0.05). 3-month treatment period of Crohn's disease has increased the iron concentration from 6.98 microg/dl to 9.95 mg/dl although the absence of supplementation (p < 0.05). In group II more often than in group I risk factors of anemia like changes in the upper gastrointestinal tract, the location of the ileum, intestinal villous atrophy and the use of immunosuppressive drugs were observed (p < 0.05). Anemia and iron deficiency were more often observed in the ileocolonic location than when the upper gastrointestinal tract was involved (adquately 55.5% vs 30.5%; p < 0.05 and 75.0% vs 41.6%; p < 0.05).