A hydrodynamic bearing device includes a sleeve having a bearing hole, a shaft, and a flange cover. The shaft is disposed in the bearing hole of the sleeve in a state of being capable of relative rotation, and has a large diameter flange portion. The flange cover is disposed opposite the bottom surface of the flange portion. A bubble suppression portion, which is formed as a recess on the bottom surface of the shaft, communicates with the upper surface of the flange portion through a communicating hole in the flange portion. This provides a hydrodynamic bearing device with which negative pressure is prevented from being generated in the bearing even when it is subjected to impact or vibration, and durability and reliability can be enhanced, as well as a spindle motor and a recording and reproducing apparatus equipped with this hydrodynamic bearing device.