Traceability (sometimes called chain-of-custody) systems are normally used to ensure that the product sold as certified is also a product that is certified. To make sure the product sold is what you promise to the end user traceability requirements are most often designed to verify that no mixing or substitution is made from source to end user. For each step in the chain, it is important to make sure that each company's procedures and operations work effectively.

The key elements in most product traceability systems verify that no mixing or substitution occur. These include audit procedures that include:

Physical or temporal segregation is used to make sure that certified and uncertified material being processed in the same operation are not substituted or mixed.
Mass balance is calculated to verify that the output amounts are consistent with the inputs.

Physical segregation means that certified products are processed in a separate machine, processing line or facility. This way only certified inputs go in and therefor only certified outputs come out. Temporal segregation means that different times at a processing facility are used to process a batch of either certified or uncertified material so that at any point in time it is clear whether or not the outputs at any point are certified.

To make sure that it all works, auditors or inspectors need to see the facility in operation.

In most cases traceability system are designed as part of a larger program to achieve social, environmental, food safety or other beneficial objectives. The main objectives are normally:

To ensure that amount produced is equal to or greater than the amount sold and,
To assure customers that the item they purchase is the same item produced in the beneficial manner.

There are a few ways in which traceability is maintained or monitored, these include: (Note: no single scheme uses all of these.)

One up, one down. This requires each participant in the value chain to have auditable records for purchases and sales of certified material. This enable auditors to make sure that the total volume of material is accounted for coming in and going out.
Whole chain traceability. Increasingly schemes are beginning to employ this approach by using a central database in which all transactions of certified material are recorded on a central database. This allows auditors and scheme managers to see the entire chain of custody for a single batch of a product. This means that a fish can have a code on it which allows you to see the date on which it was caught, the boat that caught it and each sale of that fish until it landed on your plate in a restaurant. For fully operational systems this would apply to all material in a system, not just a sample.
Mass Balance. In these systems segregation is not necessary since the entire production of a processor is subject to a percentage based claim in which they state that X% of their product is certified but no single product is identified as fully certified. If a processor buys 60% of its raw material as certified then it claims on all it product that the company uses 60% certified material in its production.
Certificate swapping. This is like emissions trading - if one processor in wants to sell product as certified then it 'swaps' certificates with a processor who has purchased certified material. The goal here is that the total sale of certified material does not exceed the amount of certified material sold globally.
Batch verification. In some cases the verification is done by just checking a set number of batches in a processor's facility. This does not include a system audit but looks at the operation of the facility. Normally this approach is used for a supplementary system when the processor is already subject to a full tractability audit for another system.
Verification audits. In addition to the traceability rules that are audited most schemes employ some method of verification outside the audits themselves. Some schemes use DNA testing to verify the species that are traded to check for substitution. Increasingly food traceability systems can used trace minerals found in food to determine where it was grown. These verification audits are used to double check the quality and reliability of the site audits done for individual certificate holders in a long or complicated value chain.

The choice of which model to follow is normally taken based on the goals of the certification scheme, the way the industry is structured and how a positive change can be best encouraged. For example an industry where the main product is sold as a bulk commodity and processing is continuous (let's say solar power sold through a public electricity grid) the choice may be to use either a mass balance or certificate swapping approach. When it is crucial that the final consumer receive a product produced in a particular way (let's say an organic pepper) then the choice may be between one up,one down and whole chain traceability.

While many systems rely on a certified traceability system (that is each link in the value chain is certified to maintain the chain of custody) there are other options. Some schemes may choose to maintain traceability using periodic inspections that are mandated through licensing contracts that allow product claims or logo use.

There have been failures in most if not all traceability systems. As mentioned in other posts, certification relies on certificate holders wanting to do a good job and in the vast majority of cases this works. These systems are not immune to fraud and there have been cases where that has occurred. In all the cases that I am aware of the rate of fraud and as well as accidental mixing or substitution in well managed traceability systems is significantly lower than for the same type of product is that is not audited or inspected for traceability.

One of the challenges to schemes that employ traceability is that a pure traceability audit does not assure much about the processor. By a pure traceability system I mean one that only focuses on maintaining at traceable link to the primary production standard and ignores all other factors. While this is a simple approach it also has the risk that certified material might be processed by children or slaves. We are beginning to see traceability systems evolve to capture more that just traceability with a growing focus on working conditions and environmental performance.

If your scheme is looking to employ a traceability or chain of custody system as part of your system it is important to consider both your options and the implications of those options on your objectives.