A probe cover system for improving comfort when using medical instruments with probes. The probe cover system generally includes a probe cover adapted for use on the probe of a medical instrument such as an otoscope or thermometer. The probe cover includes a wide inner end and a narrow outer end. The outer end includes a first opening and the inner end includes a second opening, with the first opening generally being narrower than the second opening. The probe cover includes a plastic outer layer and a cushioned, foam inner layer to improve the comfort of the patient while the medical instrument is in use.