Recommendations for screening for maternal infections and interventions to prevent disease in the fetus or newborn have been in place in Puerto Rico for more than 10 years. However, compliance with these recommendations has not been widely documented. We evaluated compliance with rubella/hepatitis B prenatal screening and vaccination recommendations, assessed hospital screening practices for syphilis and HIV, and determined risk factors for suboptimal prenatal care. Records of a random, stratified sample of 2003 pregnant women delivering in eight maternity hospitals in Puerto Rico in 2002 were reviewed. Obstetric prenatal and postnatal records were also reviewed when rubella/hepatitis B surface antigen (HBsAg) screening was not available at the hospital, and to document rubella postpartum vaccination (PPV). Prenatal screening rates were 98.4% for rubella and 98.8% for HBsAg. Overall, 5.4% [95% CI 4.4, 6.5] of women were susceptible to rubella. No eligible women received rubella PPV at the hospital and only 1.5% had documented rubella vaccine prescription at the obstetric records. Only one woman was found to be HBsAg positive and her newborn was adequately treated. However, only 0.9% newborns born to mothers with unknown HBsAg status received hepatitis B vaccine. Screening was documented in 85.7% of the hospital records for HIV and 87.9% for syphilis. Suboptimal prenatal care was more likely among teenagers, low-educated women, and women with >3 previous pregnancies. Screening rates for rubella and hepatitis B were high; however, implementation of recommendations for prevention of rubella and hepatitis B needs to be improved.