To estimate the prevalence of common mental disorders (CMD) and factors associated with these disorders among pregnant women of low socio-economic status (SES) in São Paulo. We performed a cross-sectional study with 831 women in their 20th to 30th weeks of pregnancy, who were attending antenatal clinics in primary care in São Paulo, Brazil. CMD were assessed with the Clinical Interview Schedule-Revised. Crude and adjusted prevalence ratios and 95%CI were calculated to examine the association between CMD and exposure variables. The prevalence of CMD was 20.2% (95%CI 17.5 to 23.0). Age at current pregnancy and at first delivery, current obstetric complications, not having friends in the community, living in a crowded household, lower occupational status and history of previous psychiatric treatment were all independently associated with increased prevalence of CMD. CMD is highly prevalent among pregnant women of low SES seen in primary care settings in São Paulo. A combination of distal and proximal psychosocial factors increase the risk for CMD. Primary health care professionals need to be aware of how common CMD in such settings and properly trained to deal with CMD during pregnancy.