An apparatus for automated sampling of a specimen container having a closure sealing the interior of the specimen container from the environment, comprising: a rack holding the specimen container; a sampling device having a needle, a chamber in fluid communication with the needle, and a port in fluid communication with the chamber, wherein the sampling device includes a flexible sheath covering the needle which pushes against a cap of the specimen container to prevent the needle from binding to the cap; a robotic transfer mechanism moveable relative to the rack, the robotic transfer mechanism comprising a multi-axis robot arm; a sample removal apparatus attached to the robotic transfer mechanism having gripping features for gripping the sampling device, wherein movement of the sample removal apparatus is controlled by the robotic transfer mechanism; and a pneumatic system comprising a pump located on the robotic transfer mechanism and coupled to the port of the sampling device, the pneumatic system operative to draw a portion of a sample contained within the specimen container into the chamber of the sampling device via the needle, the pneumatic system further comprising a first tube having a first end connected to the pump and a second end connected to the port of the sampling device, and a second tube having a first end connected to the pump and a second end connected to the gripping features; wherein the sample removal apparatus and robotic transfer mechanism are moveable relative to the specimen container so as to automatically insert the needle of the sampling device through the closure of the specimen container to thereby vent an interior of the specimen container and obtain equilibrium between the interior of the specimen container and the atmosphere. a rack holding the specimen container; a sampling device having a needle, a chamber in fluid communication with the needle, and a port in fluid communication with the chamber, wherein the sampling device includes a flexible sheath covering the needle which pushes against a cap of the specimen container to prevent the needle from binding to the cap; a robotic transfer mechanism moveable relative to the rack, the robotic transfer mechanism comprising a multi-axis robot arm; a sample removal apparatus attached to the robotic transfer mechanism having gripping features for gripping the sampling device, wherein movement of the sample removal apparatus is controlled by the robotic transfer mechanism; and a pneumatic system comprising a pump located on the robotic transfer mechanism and coupled to the port of the sampling device, the pneumatic system operative to draw a portion of a sample contained within the specimen container into the chamber of the sampling device via the needle, the pneumatic system further comprising a first tube having a first end connected to the pump and a second end connected to the port of the sampling device, and a second tube having a first end connected to the pump and a second end connected to the gripping features; wherein the sample removal apparatus and robotic transfer mechanism are moveable relative to the specimen container so as to automatically insert the needle of the sampling device through the closure of the specimen container to thereby vent an interior of the specimen container and obtain equilibrium between the interior of the specimen container and the atmosphere.