Pregnancy is associated with HPV infection and with Chlamydia trachomatis (CT) infection mostly due to the natural immunosuppression. In addition, pregnancy associated to CT infection can lead to adverse conditions to the woman and fetus, and CT is also believed to be a co-factor in human immunodeficiency virus infection and HPV-induced cervical cancer. The aim of this study was to establish the odds ratios (OR) of CT infection in to HPV-infected pregnant women and vice versa of women stratified by age (<25 years) and marital status. This work is part of a national multicentric transversal study carried out in six Brazilian cities supported by the Ministry of Health of Federal Government of Brazil in 2003. Cervical scrapes of 371 pregnant women were sampled. We performed a hybrid capture-2 technique to diagnose these samples on HPV and CT infection, and the women responded a questionnaire. Significant association was observed between nonstable marital status and hr-HPV infection [OR = 2.61 (1.38-4.97) P = 0.003)], and age <25 years old [OR = 2.26 (1.09-4.71) P = 0.029]. Nonstable marital status was also associated with lr-HPV infection [OR = 2.67 (1.59-4.50) P < 0.001), and age <25 years old [OR = 2.55 (1.51-4.32) P < 0.001). Fifty of the 371 pregnant women were infected with hr-HPV (13.5%) and 111 (30.0%) were infected with lr-HPV. The coinfections of HPV and CT were found in 31 women, that is, 8.36% of the pregnant women (P < 0.001). The high rate of simultaneous CT and HPV infection in pregnant women favors the recommendation to screen pregnant women for both CT and HPV.