Atopic disease is associated with chronic inflammation, and anemia has been reported in patients with inflammatory disorders such as rheumatoid arthritis, chronic obstructive pulmonary disease, and irritable bowel disease. The objective of this study was to determine whether atopic disease is associated with an increased risk of anemia. A cross-sectional study with propensity score weighting was conducted using a health insurance review agency claims dataset comprised of randomized patients who used the Korean national health system at least once in 2016. The association between atopic disease (asthma, atopic dermatitis, allergic rhinitis) and anemia (iron deficiency anemia (IDA) and/or anemia of inflammation (AI)) was examined. A total of 1,468,033 patients were included in this study. The IDA/AI prevalence was 3.1% (45,681 patients). After propensity score weighting, there were 46,958 and 45,681 patients in the non-anemic and anemic groups, respectively. The prevalence of IDA/AI in patients with atopic dermatitis, allergic rhinitis, or asthma had an odds ratio (OR) of 1.40 (95% confidence interval (CI), 1.33–1.48; p < 0.001), 1.17 (95% CI, 1.14–1.21; p < 0.001), and 1.32 (95% CI, 1.28–1.36; p < 0.001), respectively. In addition, the prevalence of IDA increased with higher numbers of atopic diseases. In conclusion, the prevalence of IDA/AI was higher in patients with atopic disease, even after adjusting for demographic characteristics and other risk factors. Further study is needed to distinguish between IDA and AI and to enhance understanding of the etiology of anemia in patients with inflammatory conditions.