Background One of the main drawbacks of synthetic, non-viral gene vectors is their relatively low in vivo efficiency when compared with viral vectors. The present paper describes the use of a partially fluorinated glycerophosphoethanolamine (F-PE), a close analog of DOPE, which, as a helper lipid with the cationic lipopolyamine pcTG90, increases its in vitro and in vivo gene transfer capability to a larger extent than DOPE. Methods To evaluate the contribution of F-PE to lipoplex-mediated gene transfer, the effect of including F-PE in lipoplexes formulated with the lipopolyamine pcTG90 for various pcTG90/DOPE/F-PE molar ratios [1 : (1-x) : x; 1 : (2 - y) : y] was examined. For the in vitro analyses on human lung carcinoma epithelial A549 cells, the lipoplexes were formulated with the luciferase reporter plasmid pTG11033 using various N/P ratios (from 10 to 0.8, N = number of pcTG90 amines, P = number of DNA phosphates). The in vivo analyses were performed (1) with the luciferase reporter plasmid pCMV-Luc, which gives higher luciferase expression in the lung than pcTG11033; (2) with pcTG90/co-lipid(s) (1:2) lipoplexes which yield higher expression than the (1:1) formulations; and (3) by intravenous (iv) injection into the tail vein of mice. Results The efficiency of the F-PE lipoplexes to transfect in vitro A549 cells was significantly higher (5-90-fold) than that of DOPE lipoplexes, when formulated in HEPES. However, when formulated in 5% glucose, both co-lipids display a comparable transfection helper potential. Most remarkably, an up to eight-fold increase of luciferase expression could be measured in the lung after iv injection of pcTG90/F-PE (1 : 2) N/P 5 lipoplexes as compared with the pcTG90/DOPE lipoplexes. It led also to higher luciferase expression than PEI (ExGen500)/pCMV-Luc N/P 10 polyplexes. Besides expression in lung, low levels of luciferase expression were also observed in heart, spleen and liver. Conclusion The present work, showing a higher in vitro and in vivo transfection potential for lipoplexes formulated with a partially fluorinated co-lipid as compared with its analogous DOPE lipoplexes or PEI polyplexes, indicates that 'fluorinated' lipoplexes are attractive candidates for in vivo applications. Copyright (C) 2001 John Wiley & Sons, Ltd.