(covers information from several alternate timelines)
Decontamination is a process for removing dangerous substances from objects or people. During the 22nd century, with transporter technology in its infancy and most off-world missions carried out by shuttlecraft, this process was carried out by applying special gels and creams to the skin surface; sickbay was equipped with a decontamination chamber for this purpose. (ENT: "Broken Bow")
In 2258 of the alternate reality, despite James T. Kirk dying inside the warp core, Montgomery Scott cautioned Spock not to open the door, as the decontamination process was incomplete and opening it now would flood the entire compartment with radiation, adding that the door was locked. (Star Trek Into Darkness)
As of the 24th century, decontamination is completely integrated into the transport process; harmful substances such as viruses and microorganisms are automatically removed during transport, essentially subtracted from the transporter's internal representation of the transported object or person. However, decontamination in transport is not always effective, such as the case of polywater intoxication. (TNG: "The Naked Now", "Shades of Gray")
Decontamination is generally only effective against known hazards, or classes of hazards. Unknown hazards have some chance of avoiding decontamination; this chance depends on the degree to which they are similar to known hazards. This is true regardless of the specific method used.