A retrospective survey estimating the prevalence of hepatitis viruses B (HBV) and C (HCV) was conducted on samples taken in 1,002 African pregnant women (501 diagnosed as HIV-1 positive and 501 HIV-1 negative) participating in a clinical trial program conducted in Abidjan, Côte d'Ivoire (West Africa). Hepatitis B markers studied were HBs antigen (HBsAg), and if positive, HBe antigen/anti-HBe antibodies and HBV DNA. Two third generation (G3) HCV enzyme immunoassays (EIAs) were used for primary HCV screening. All anti-HCV antibody-positive sera were assessed further with supplementary assays (one another G3 EIA, RIBA 3.0, and HCV RNA). HCV genotypes were also determined. HBsAg was found in a similar proportion among HIV-positive (45/499, 9.0%, 95% confidence interval [95% CI], 6.6-11.9) and HIV-negative (40/498, 8.0%, 95% CI, 5.8-10.8) women (P = 0.58). The diagnosis of chronic hepatitis B, based on HBV DNA positive results, was more frequent in HIV-positive women (26.7%), compared to HIV-negative women (9.4%) (P = 0.06). In the case of hepatitis C infection, after supplementary testing allowing the elimination of frequent false-positive screening results, a prevalence rate of about 1% was found, both in HIV-positive (6/501, 1.2%, 95% CI, 0.44-2.59) and HIV-negative (4/501, 0.8%, 95% CI, 0.22-2.03) women (P = 0.53). Of the 10 samples confirmed positive and assessed for HCV RNA, eight (80%) were viraemic and belonged to HCV genotypes 1 or 2. The relative high frequency of HIV/HBV coinfection in Côte d'Ivoire emphasises the need for monitoring the risk of hepatotoxicity by antiretroviral therapy in such patients. We propose an accurate and cost-efficient algorithm for HCV diagnosis in Africa.