The novel coronavirus pneumonia (NCP) has spread from Wuhan to all parts of China since December 2019, and the prevention and control of NCP is a top priority for medical staff. Now report three cases of NCP patients, whose viral nucleic acids still positive in stool after throat swab detection turned negative. In view of the highly homologous and similar clinical manifestations between the 2019 novel coronavirus (2019-nCoV) and the severe acute respiratory syndrome(SARS) related coronaviruses, it is recommended to attach great importance to the detection of the viral nucleic acids in stool, with the reference of SARS prevention and control experience. In order to minimize the risks of gastrointestinal spread, the detection of 2019-nCoV nucleic acids in stool may be recommended as the reference standard of disisolation and discharge.