Introduction: Anemia is a public health problem, more serious during pregnancy, and information in this sense regarding women of short stature is not available. Objective: To compare the proportion of anemia in pregnant women with and without short stature. Methods: A cross-sectional study was carried out in which were used 1 555 847 records of pregnant women from the System of Information on Nutrition Status of the Food and Nutrition Center of the National Health Institute from 2009 to 2013. These women had been evaluated in health facilities of the Peruvian Ministry of Health. Pregnant women with short stature (≤ 1.40 cm) and anemia (Hb < 11 g/dL) were evaluated, with hemoglobin corrected for altitude. Results: 2.2 % presented short stature. 89.6 % were from 15 to 35 years old. 30.1 to 33.7 % of the pregnant women with short stature presented anemia, and 25.1 to 27.5 % of pregnant women without short stature. In this study were enrolled pregnant women with short stature and anemia, age from 11 to 14 years (PR: 2.2 CI 95% 1.9-2.6), being in the third trimester of pregnancy (PR: 1.2 CI 95% 1.1-1.2), whom were attended at a health post (PR: 1.3 IC95% 1.3-1.4), living in the mountains (RP: 2.4 IC95% 2.3-2.5), in rural areas (RP: 1.9 IC95% 1.8-2.0), quintile 1 (RP: 2,3 IC95% 2,2-2,4) and with an altitude from 3 001 to 4 000 meters above the sea level (RP: 2,5 IC95 % 2.5-2.7). Conclusions: Pregnant women with short stature have a higher proportion of anemia than those without short stature, which is mainly associated with adolescence, living in rural areas of the highlands and with quintile 1 of poverty.