Multi-walled carbon nanotubes (MWCNT) were used to separate amoxicillin from aqueous media. The parameters affecting amoxicillin adsorption such as pH, temperature, time, interferences of similar molecules, and the amount of adsorbent used were studied. Amoxicillin adsorption using MWCNT was compared to that using Fullerene C60 and activated carbon (AC). The adsorption efficiency of 0.1 and 0.2 g of MWCNT using in a continuous mode were 86.5% and 87.9%, respectively. Evaluation of the adsorbent capacity showed that each gram of MWCNT can absorb 22.9 mg amoxicillin. The effect of pH was studied over the range 2-8 and revealed that adsorption of the amoxicillin at the initial pH of 4.6 was more effective than any other pH. The adsorption of amoxicillin on MWCNT was much greater than Fullerene C60 and AC. Adsorption data showed that they were best fitted to the Langmuir isotherm.