In this study, we used a solution of FeCl(3) in THF to facilitate the Mannich-type reaction of aldehyde, amine and phosphite compounds to form corresponding alpha-aminophosphonates in a one-pot, three-component reaction. Selected alpha-aminophosphonates were entered into a biological assay test and were studied by docking methods, using Autodock 3.0. The results showed that the reactions were carried out mildly and eco-friendly to form alpha-aminophosphonates in high yields. Some were found to have cytotoxic activity on the cell lines RAJI, JURKAT and MCF-7. An indole derived bis(alpha-aminophosphonates) showed maximum cytotoxic effect comparable to doxorubicin. Although the FDE (Final Docking Energy) for the most cytotoxic compound was of the most negative value, there is no correlation between FDE and cytotoxicity.