In the last twenty years, the occurence of pharmaceuticals in enviroment has become a burning ecological issue. One of these pharmaceuticals is 5-fluorouracil (5-FU), antimetabolite drug which has been found in the enviroment in concentrations up to 63 ng/L. In this work, it is experimentaly shown that during the chlorination process, which is one of the most common method for wastewater treatment, the 5-FU yields chlorohydrine product 3a. Structural characteristics of 3a are determined using 1H, 19F i 13C NMR spectroscopy. Reaction mechanism of chlorination of 5-fluorouracil is investigated using quantum chemistry methods. M062X functional with 6-311+G(d) basis set is applied. The solvent effects are described by the implicit SMD solvation model, using the optimal number of the explicit solvent molecules (H2O). It has been shown that 5-FU is chlorinated at the C5 position in the pyrimidine ring. The two steps reaction in which the first step is the addition of Cl+ on 1-N1 anion, yielding the imine intermediate 4, is determined as the most possible reaction mechanism. The energy barrier which corresponds to the addition of chloronium ion (through the transition state structure TSI) is 106,8 kJ/mol. The addition of water on the imine intermediate (Gǂ = 26,7 kJ/mol), which results in the chlorohydrine 3a, is the second reaction step. The results obtained with quantum chemical methods are in agreement with experimental data. Results of these study play a key role in predicting the ecological fate of 5-FU.