The current revolution in biomedical sciences has raised new hope for early diagnosis, prevention, and treatment of human diseases. Recent advancements in genomics, proteomics, and other basic sciences are currently transforming the medical science, and offer the promise of answering many of the questions related to human diseases, including their early and accurate diagnosis. Profiling of biological fluids (i.e., serum, urine, amniotic fluid, and cerebrospinal fluid) has successfully identified relevant protein biomarkers that potentially can change early diagnosis and treatment of several medical conditions related to human pregnancy. Similarly, proteomics holds the promise to complement genomics to revolutionize screening and prenatal diagnosis of genetic conditions during early pregnancy. This article summarizes current technology and reviews the application of proteomics in diagnosis of genetic disorders during human pregnancy.