A flow-through vapor phase decontamination apparatus includes at least one isolator unit (14) defining an isolation chamber (16) that receives a load (L) for decontamination. The apparatus includes a vapor phase decontaminant generation system (20) integrally connected to the at least one isolator unit (14). The vapor phase decontaminant generator system (20) includes one or more vaporizers (22) that inject a combination of a carrier gas and a vaporized decontaminant such as H.sub.2 O.sub.2 into the isolation chamber (16). A blower (24) recirculates the carrier gas through the one or more vaporizers (22) for replenishment of the decontaminant vapor. Alternatively, an automated filling system (70a-70c) is provided within the isolation chamber (16) for aseptic filling of containers (C). A conveyor system (68) transports the containers (C) into and out of the isolation chamber (16). The decontamination apparatus includes an electronic control system (26) for controlling decontamination operations.