A filter device which is installed in a flow path and filters foreign substances from a gas which flows through the flow path to which a pressure selectively switched between a negative pressure and a positive pressure is supplied, wherein the filter device comprises a first port for selectively switching between and inputting a negative pressure and a positive pressure; a second port for outputting to an outside the negative pressure and the positive pressure inputted from the first port; and a negative pressure-side filter and a positive pressure-side filter which are disposed between the first port and the second port, and connected in parallel to the first and second ports (20, 30), wherein the negative pressure-side filter has a breathable negative pressure-side filter element to filter foreign substances from a gas which flows from the second port to the first port, and the positive pressure-side filter has a breathable positive pressure-side filter element to filter foreign substances from a gas which flows from the first port to the second port, wherein a shuttle valve is disposed between the first port, and the negative pressure-side and positive pressure-side filters (4, 5), and wherein the shuttle valve has a first valve opening which communicates with the first port, a second valve opening which communicates with the negative pressure-side filter, and a third valve opening which communicates with the positive pressure-side filter, characterized in that a valve disc switches between communication states of the valve openings (70, 71, 72) by a pressure difference of a gas in the valve openings (70, 71, 72), and that the valve disc is a single valve disc reciprocating between a position where, when a negative pressure is supplied to the first port, the valve disc opens communication between the first port and the negative pressure-side filter through the first valve opening and the second valve opening to output the negative pressure from the second port, and simultaneously blocks communication between the first port and the positive pressure-side filter through the first valve opening and the third valve opening, and a position where, when a positive pressure is supplied to the first port, the valve disc opens communication between the first port and the positive pressure-side filter through the first valve opening and the third valve opening to output the positive pressure from the second port, and simultaneously blocks communication between the first port and the negative pressure-side filter through the first valve opening and the second valve opening. wherein the filter device comprises a first port for selectively switching between and inputting a negative pressure and a positive pressure; a second port for outputting to an outside the negative pressure and the positive pressure inputted from the first port; and a negative pressure-side filter and a positive pressure-side filter which are disposed between the first port and the second port, and connected in parallel to the first and second ports (20, 30), wherein the negative pressure-side filter has a breathable negative pressure-side filter element to filter foreign substances from a gas which flows from the second port to the first port, and the positive pressure-side filter has a breathable positive pressure-side filter element to filter foreign substances from a gas which flows from the first port to the second port, wherein a shuttle valve is disposed between the first port, and the negative pressure-side and positive pressure-side filters (4, 5), and wherein the shuttle valve has a first valve opening which communicates with the first port, a second valve opening which communicates with the negative pressure-side filter, and a third valve opening which communicates with the positive pressure-side filter, characterized in that a valve disc switches between communication states of the valve openings (70, 71, 72) by a pressure difference of a gas in the valve openings (70, 71, 72), and that the valve disc is a single valve disc reciprocating between a position where, when a negative pressure is supplied to the first port, the valve disc opens communication between the first port and the negative pressure-side filter through the first valve opening and the second valve opening to output the negative pressure from the second port, and simultaneously blocks communication between the first port and the positive pressure-side filter through the first valve opening and the third valve opening, and a position where, when a positive pressure is supplied to the first port, the valve disc opens communication between the first port and the positive pressure-side filter through the first valve opening and the third valve opening to output the positive pressure from the second port, and simultaneously blocks communication between the first port and the negative pressure-side filter through the first valve opening and the second valve opening.