Pregnant women are the most vulnerable populations exposed to intestinal parasitoses. To develop strategies to fight against these infections, it is essential to carry out regular surveys in order to provide reliable epidemiological data on intestinal parasitoses in at-risk populations. A prospective cross-sectional study was carried out from February to April 2015 in pregnant women seen during the prenatal consultation. The study took place in 3 health centers located in Health District of Dafra at Bobo-Dioulasso in Burkina Faso. The parasitological examination consisted in carrying out a standard stool parasitological examination and the modified Ziehl Neelsen staining. A total of 315 stool samples were collected and analyzed. The overall prevalence of intestinal parasitosis was 66.7% [95% CI: 61.1–71.8] with prevalences of 60.9% in Bolomakot., 69.2% in Guimbi and 69.8% in Y.gu.r.sso. Protozoa were the most encountered with of 66.0% prevalence and 1.3% of helminths. The most common protozoa species were Entamoeba coli (36.2%), Giardia lamblia (16.2%), Entamoeba histolytica (14.9%), Cryptosporidium sp. (12.1%) and Trichomonas intestinalis (10.5%). The helminths were represented by Hymenolepis nana (0.6%), Strongyloides stercoralis (0.3%) and Dicrocoelium sp. (0.3%). The prevalence of intestinal parasitosis is very high in pregnant women and dominated by protozoa. Most recently, it has been shown that metronidazole can be administered at all ages of pregnancy at a dosage of 1 g/day for 5 days for the treatment of intestinal protozoa in pregnant women. It would therefore be essential to evaluate this strategy in Burkina Faso by administering metronidazole concomitantly with sulfadoxine-pyrimethamine.