An automated sample processing system comprising: a sample processing instrument configured to handle samples collected in differently shaped sample collection receptacles, the sample processing instrument comprising a first automated pipettor configured to aspirate at least a portion of a sample from a first sample collection receptacle and dispense the portion of the first sample into a first processing receptacle; a first assay instrument comprising a second automated pipettor configured to aspirate at least portions of samples from processing receptacles containing samples at a first processing position within the first assay instrument and dispense at least portions of samples into assay receptacles, the first assay instrument being further configured to perform first assays on the portions of the samples contained within assay receptacles; a first conveyor assembly configured to transport a first carrier coupled to the first processing receptacle containing the portion of the first sample dispensed by the first automated pipettor from the sample processing instrument to a first position outside the sample processing instrument; a second conveyor assembly configured to receive the first carrier coupled to the first processing receptacle from the first conveyor assembly at the first position outside the sample processing instrument, and to transport the first carrier to a second position outside the first assay instrument; a third conveyor assembly configured to (i) receive the first carrier from the second conveyor assembly at the second position outside the first assay instrument, (ii) transport the first carrier to the first processing position within the first assay instrument at which the second automated pipettor of the first assay instrument aspirates at least a portion of the first sample from the first processing receptacle for subsequently dispensing the portion of the first sample into an assay receptacle, (iii) after the second automated pipettor of the first assay instrument aspirates at least a portion of the first sample from the first processing receptacle, transport the first carrier coupled to the first processing receptacle from the first processing position to a third position outside the first assay instrument, and (iv) transfer the first carrier at the third position outside the first assay instrument to the second conveyor assembly. a sample processing instrument configured to handle samples collected in differently shaped sample collection receptacles, the sample processing instrument comprising a first automated pipettor configured to aspirate at least a portion of a sample from a first sample collection receptacle and dispense the portion of the first sample into a first processing receptacle; a first assay instrument comprising a second automated pipettor configured to aspirate at least portions of samples from processing receptacles containing samples at a first processing position within the first assay instrument and dispense at least portions of samples into assay receptacles, the first assay instrument being further configured to perform first assays on the portions of the samples contained within assay receptacles; a first conveyor assembly configured to transport a first carrier coupled to the first processing receptacle containing the portion of the first sample dispensed by the first automated pipettor from the sample processing instrument to a first position outside the sample processing instrument; a second conveyor assembly configured to receive the first carrier coupled to the first processing receptacle from the first conveyor assembly at the first position outside the sample processing instrument, and to transport the first carrier to a second position outside the first assay instrument; a third conveyor assembly configured to (i) receive the first carrier from the second conveyor assembly at the second position outside the first assay instrument, (ii) transport the first carrier to the first processing position within the first assay instrument at which the second automated pipettor of the first assay instrument aspirates at least a portion of the first sample from the first processing receptacle for subsequently dispensing the portion of the first sample into an assay receptacle, (iii) after the second automated pipettor of the first assay instrument aspirates at least a portion of the first sample from the first processing receptacle, transport the first carrier coupled to the first processing receptacle from the first processing position to a third position outside the first assay instrument, and (iv) transfer the first carrier at the third position outside the first assay instrument to the second conveyor assembly. (i) receive the first carrier from the second conveyor assembly at the second position outside the first assay instrument, (ii) transport the first carrier to the first processing position within the first assay instrument at which the second automated pipettor of the first assay instrument aspirates at least a portion of the first sample from the first processing receptacle for subsequently dispensing the portion of the first sample into an assay receptacle, (iii) after the second automated pipettor of the first assay instrument aspirates at least a portion of the first sample from the first processing receptacle, transport the first carrier coupled to the first processing receptacle from the first processing position to a third position outside the first assay instrument, and (iv) transfer the first carrier at the third position outside the first assay instrument to the second conveyor assembly.