Lipids of biogenic and anthropogenic origin were determined in aerosol samples, collected seasonally, in a coastal area on the north of the island of Crete. Lipid classes such as n-alkanes, hopanes, polycyclic aromatic hydrocarbons, fatty alcohols, fatty acids, fatty acid salts and α,ω-dicarboxylic acids were characterized by GC/MS and GC/FID analysis, in terms of their contents of homologous compound series. The concentrations ranged between 56 and 215 ng m−3 for n-alkanes, 10 and 52 ng m−3 for polycyclic aromatic hydrocarbons, 2 and 31 ng m−3 for fatty alcohols, 13 and 279 ng m−3 for fatty acids, 24 and 220 ng m−3 for fatty acid salts and 0.4 and 7.5 ng m−3 for α, ω-dicarboxylic acid salts. The prevailing winds were influencing the composition of the eolian particles. Generally, aerosols sampled during south wind events predominantly contained lipids originating from higher plants, while when north and northwest winds prevailed the major components were of marine origin. The absence of unsaturated fatty acids in all aerosol samples is related to the presence of α,ω-dicarboxylic acids, which are believed to be their photo-oxidation products.