Alkylphospholipid (APL) analogs are a new class of membrane-directed synthetic compounds with a variety of biological actions and clinical applications. In particular, these agents are promising candidates in cancer treatment. We have demonstrated that after prolonged treatment APLs alter intracellular cholesterol traffic and metabolism in human tumor-cell lines, leading to an accumulation of cholesterol inside the cell. After further investigation concerning the mode of action of APLs, we have explored the influence of several APLs on novel aspects of cholesterol and lipoprotein homeostasis using hepatoma HepG2 cells and THP1-derived macrophages. Quantitative real-time PCR analysis with a pathway-focused PCR array system was performed to measure relative changes in the mRNA expression of a number of genes related to cholesterol transport and metabolism. We compared the gene-expression profiles of HepG2 cells treated with miltefosine, edelfosine or perifosine for 6h and 24h with the profile of control cells. We also analysed particular genes of interest in both HepG2 and macrophage-like THP1 cells using specific PCR assays. Immunoblots were used to confirm protein-expression changes. Measurement of ABCA1-mediated cholesterol efflux was determined using apoA1 as cholesterol acceptor. We found global changes in gene-expression patterns to maintain cholesterol homeostasis after exposure of cells to APLs. The pathways for cholesterol biosynthesis and LDL-cholesterol uptake were both transcriptionally upregulated by the three APLs assayed. Conversely, major pathways involved in the catabolism of cholesterol to bile acids and lipoprotein-associated cholesterol export were impaired after APL incubation, which may well contribute to the higher cell-cholesterol levels induced by these compounds. Incubation of cells with different APLs stimulated cholesterol biosynthesis and uptake at the same time as it depressed common pathways for excess cholesterol removal in tumor cells, ultimately leading to altered cholesterol homeostasis.