Intestinal parasitic infection increases the risk of developing iron deficiency anemia (IDA) during pregnancy. The objective of this study was to assess Blastocystis hominis as a contributing risk factor for development of IDA in pregnant women. A total of 200 fecal specimens from 120 pregnant women with IDA (mean Hb = 9.6 g/dl), and 80 non-anemic controls were examined for Blastocystis. Fecal specimens were examined by the formalin/ethyl-acetate concentration technique, iron hematoxylin staining, modified Ziehl-Neelsen acid-fast staining, and by the in vitro cultivation technique for Blastocystis. Frequency of Blastocystis infection, detected microscopically and by the in vitro culture technique, was significantly higher in IDA study group (n = 48; 40%) compared to non-anemic controls (n = 5; 6.3%; P < 0.0001), and 26.5% (n = 53) in all study subjects. Among the 48 cases, Blastocystis without other intestinal parasitic infections was detected in 41 cases (34.2%), while seven cases (5.8%) with Blastocystis were coinfected with other intestinal parasites which included Giardia and Cryptosporidium (1.7% each), and Entamoeba sp., Ascaris, and Trichuris (0.8% each). The mean Hb level of the 48 Blastocystis-infected cases was 9.2 g/dl (mild anemia). While the other 72 IDA cases with no infection had mean Hb of 10.0 g/dl (mild anemia), with a significant difference in mean Hb level between Blastocystis-infected and the non-infected IDA cases (P < 0.0001). Furthermore, among the 48 Blastocystis-infected IDA cases, the mean Hb of the 41 Blastocystis-infected cases without other intestinal parasitic co-infection was 9.1 g/dl (mild anemia), while the mean Hb level of the 7 Blastocystis-infected cases with other intestinal parasitic co-infection was 8.7 g/dl (moderate anemia). Findings of the current study showed that B. hominis infection contributes to the development of IDA in pregnant women. Hence, parasitological diagnostic tests are recommended in routine examination at all antenatal clinics.