Molecular dynamics simulation has been performed to investigate the structural properties of perifosine and its synthetic spin-labeled alkylphospholipid analogues. The conformations adopted by these compounds in water and in a dipalmitoylphosphatidylcholine bilayer as a function of the presence and position of the N-oxyl-4',4'-dimethyloxazolidine ring (doxyl group) have been investigated by all-atom molecular dynamics. No predominant conformation was observed in water, but the molecules adopt specific orientations and conformations in the lipid bilayer. As is expected, alkyl chains tend to insert into the hydrophobic core, while charged groups stay at the lipid-water interface. A doxyl group in the middle of the alkyl chain moves up to the interface region, thus preventing adoption of the extended conformation. Compounds with a doxyl group close to the polar head group adopt conformations similar to that of unlabeled perifosine within the first nanoseconds of simulation. When the doxyl group is at the end of alkyl chain, the spin-labeled molecule needs more time to reach equilibrium. These results indicate a considerable effect of the doxyl position within the alkyl chain on its localization in the lipid bilayer and can be extended further to other similar spin probes used in the electron paramagnetic resonance spectroscopy of biological membranes.