1,3-Propanediol (1,3-PDO) has received increasing attention due to usage as the monomer of biopolymer-polytrimethylene terephthalate (PTT) which can be produced from bioresources. For the economic production of 1,3-PDO, the deveolpment of cost effective removal process of by-products such as carboxylic acids from its fermentation broth. Amien-based extraction is the separation process using reactions between amine and materials extracted. The extractabilities for carboxylic acid increased with amine concentration and decreased with pH values. It was also observed that the removal efficiency of carboxylic acids from 1,3-PDO solution was above 90% without any coextraction of 1,3-PDO. From this work, it was found that the amine-based extraction can be promising separation process for the production of pure 1,3-PDO.