Infectious diseases resemble a great threat to the human health according to World Health Organization where about 17% of all deaths (≈9.2 million deaths) in 2013 recorded are related to infectious diseases. The pathogenic microorganisms such as bacteria, viruses, fungi and parasites are the principle causes of infectious diseases. Ebola, AIDS, dengue, hepatitis, malaria, tuberculosis and schistosomiasis are among 216 infectious diseases found where the immunity represents the first line defense in infection. Lipidomic includes examination of different biological lipids in the biological cell. The lipidomic research covers all aspects of individual lipid molecule including its structure, function, connection with other cell constituents such as protein, lipid, and metabolite in both health and disease conditions. Details of cell biology obtained from different pathogens (viruses, bacteria, and parasites) provide a great data on molecular structure of host- pathogen relation and consequently on infection process. The lipids here play a very important role in many processes involved in host-pathogen relations. The role of lipid in host-pathogen link includes many processes in (1) structural host constituents, (2) host recognition, (3) intracellular transferring, and (4) energy and resource homeostasis during pathogen duplication. There are many lipid phosphatases, kinases, and lipases molecules that greatly involved in these processes and controlling pathogen expression and infection progress. The cell lipid metabolism depends on an adequate energy stores that push the infection to be accelerated and disease symptoms to be appeared. Consequently, future lipidomics studies are the basic for detecting the lipid role in host-pathogen relations which help in therapy advances and biomarkers development.