The formation of different complexes of folic acid depending on the size of the host cyclodextrin resulting in either an exclusion compound (with the smallest α-cyclodextrin) or 2-rotaxane, where cyclodextrin is threaded over folic acid (with β- and γ-cyclodextrins), is presented. The formation is carried out in water which allows both possible application in pharmaceutical sciences and usage of environmentally friendly "green chemistry". The obtained compounds are thoroughly characterized using one and two dimensional NMR, mass spectrometry, differential scanning calorimetry and thermogravimetric analysis.