At the feto-maternal interface, trophoblast cells express membrane bound receptors; their modulation plays a vital role in achieving immune recognition and self-tolerance needed for pregnancy to develop. Trophoblasts exhibit selective expression of the HLA class la (HLA-C) and Ib (HLA-G, -E, -F) antigens and are also able to recognise pathogen associated molecular patterns (P AMPs) through TLRs. The role of these later molecules in pregnancy is not fully understood, it is likely they form the first line of defence against infection. The hypothesis derived from the above is that some selectively expressed gene products of the HLA gene family form preferential physical associations, which contribute to the function of HLA at the fetomaternal interface and the maternal recognition of the fetus. It is also hypothesised that trophoblast responses to individual bacterial or viral infection might be different from responses to dual infection and that viral infection might sensitise the trophoblast for concomitant bacterial infection. In the course of these studies a novel method that allows detection and quantification of HLA class I molecules for an accurate measurement of the degree of co localisation on trophoblast choriocarcinoma cells, ACH-3P and JEG-3 was developed. Trophoblast responses to TLR-3 ligand poly(I:C) and TLR-4 ligand LPS were investigated by monitoring cell proliferation, cytoskeletal morphology, NF-KS and COX-2 activation and nanoscale LC-MSIMS analysis of membrane proteins. Our data shows that the cell-surface HLA class I molecules HLA-G, -E and -C form preferential heterotypic associations and HLA-GIHLA-E colocalisation is induced by progesterone and lipopolysaccharide. Dual infection cause a declined cell growth, cytoskeletal alterations and differential protein expression. It is postulated that at the fetomaternal interface, both the innate and adaptive immunity are functionally modulated and this facilitates the maternal immune adjustment for the semi-allogenic fetus as well as pathogen recognition.