Functional genomics (transcriptomics and proteomics) is a global, systematic and comprehensive approach to the identification and description of the processes and pathways involved in normal and abnormal physiological states. The functional genomics methods most applied today are DNA microarrays and proteomics methods, primarily two-dimensional gel electrophoresis coupled with mass spectrometry. To date, interesting research has been carried out, representing milestones for future implementation of functional genomics/proteomics in perinatal medicine. For instance, possible biomarkers of pre-eclampsia, preterm labor and gestational trophoblastic diseases have been discovered. Further systematic examination of differentially regulated genes and proteins in maternal and fetal tissues and fluids will be required. However, high-throughput technologies reflect biological fluctuations and methodological errors. Large amounts of such different data challenge the performance and capacity of the statistical tools and software available at present. Further major developments in this field are pending and the intellectual investment will certainly result in clinical advances.