Separating rejected ballots from spoiled ballots is important since the significance of these ballots is very different. Mixing them may seriously impact the audit trail.
Spoiled ballots should never end up in the ballot box and should be secured in a sealed envelope attached to the ballot box (this is a suggested way). A spoiled ballot is generally one that a voter has inadvertently 'spoiled' by marking it incorrectly; it is handed back to poll officials in exchange for a new blank ballot that is then marked by the voter and placed in the ballot box. A spoiled ballot may also be one that is improperly printed, torn, soiled, or otherwise marked in a way that could be linked to an individual voter and does not guarantee vote secrecy.
A rejected ballot is one that has made its way into the ballot box but has been rejected because it was improperly marked, or was not marked at all when a mark was required. The most common criteria to reject a ballot are: ballot with no mark; ballot with mark for more than one candidate/political party/option when only one was supposed to be chosen; ballot marked with a type of pen or pencil other than the one provided at the polling station; unofficial mark according to the law; unusual marks; ballot marked so the voter could be identified; or ballot marked in a location prohibited by legislation (outside the circle, etc.).
In some jurisdictions, blank ballots (ballots with no marks) are counted separately (and may be considered as protest votes); in others, they are considered to be rejected ballots. In all cases, all ballots are to be kept and none should be destroyed at this stage of the electoral process.
In countries using envelopes, since no marks are made on the ballot itself, the identification of a rejected ballot from a valid ballot is different. For example, a rejected ballot will be an envelope in which there will be two ballots; an empty envelope; a ballot in an envelope marked in a way that the secrecy of the voter is compromised; etc.
In many jurisdictions, if the intention of the voter is clear, all types of marks can be accepted. In others, the legislation is very clear on which specific types of marks are to be accepted, even on a write-in ballot (see Examples of laws and regulations - Philippines). For these specific cases, those marks should be clearly demonstrated during the training of counting officials and documented in their manual (see Manual - South Africa) or in the operational guideline to help the counting official in making his decision.
A card summarising the marks to be accepted or rejected, with pictures of sample ballots showing those marks, is a very useful tool that can be inserted in the counting officials' training kit (see Quick reference - counting centres - Bangladesh).