Background Intestinal parasitism in large urban cities is an ongoing public health challenge. Although most epidemiological studies were concentrating on children, there is an ongoing concern that adult vulnerable populations are prone to protozoal and helminthic pathogenic infestations. In pregnant women living in social inequality settings, this is particularly important as it may affect their overall health and that of their offspring. Methods We investigated the prevalence of intestinal parasitic infections in pregnant women in three districts of Bogotá, the largest city in Colombia. We undertook a cross-sectional study including questionnaires on sociodemographic factors and living conditions, in addition to home visits. By examination of stool samples, we determined the prevalence of intestinal parasites, including protozoa and helminths that are pathogenic and of debated pathogenicity. The presence of microorganisms was detected by multiple approaches including direct smears, concentration techniques, double stool sampling and/or qPCR techniques. Five hundred and fifty pregnant women from low-income urban areas participated in this study by answering the questionnaire, with 331 providing in addition a stool sample, 98 of them providing two stool samples, and 48 of them being prospectively analyzed for the presence of protozoal and helminthic parasites with quantitative PCR. Results The findings revealed an overall 41.4% prevalence of intestinal parasites, with an unexpected 40.5% predominance of protozoa that are considered non-pathogenic and/or of debated pathogenicity, withBlastocystis hominis as the most prevalent parasite (25.1%). The low prevalence of pathogenic parasites was confirmed with all techniques. Double sampling and qPCR showed highest diagnostic capacity. Sociodemographic, pregnancy and living conditions analyses in women infected with any parasite revealed associations with civil status (higher parasites in married women or those living with someone, P < 0.038) and with last deworming (higher when deworming was done over a year ago, P < 0.018). Higher trends were found between intestinal polyparasitism and women from minority groups and those not having water sinks. Conclusions This is the first study focused on pregnant women in Bogotá, the largest city in Colombia that estimates the prevalence and factors associated with intestinal parasitism in vulnerable populations living in conditions of poverty and social inequality. Although a low prevalence of pathogenic parasites was found in pregnant women, a high prevalence of parasites with disputed pathogenicity was revealed. In Bogotá, the good quality of water for human consumption, open availability of broad-spectrum anti-parasitic drugs, better educational level and appropriate sanitary facilities play an important role in the prevention of pathogenic parasitic infections. However, the high prevalence of non-pathogenic parasites indicates that fecal-oral contamination continues in these communities. Accordingly, public health services should emphasize education campaigns to prevent these contamination routes, particularly in women belonging to minority groups, those without water sinks and who have not been dewormed recently. Additionally, public health services could take into account the findings that double stool sampling may increase diagnostic capacity in these populations, a cost-effective strategy in middle income countries like Colombia.