In per-protocol analysis, patients who don't complete the study are excluded from the final analysis. However, this can not only create a lot of false conclusions but also disrupt the randomization of the study groups.
For example, if you were studying the effects of a new obesity drug on a group of patients, but some were excluded from the final analysis due to side effects, you may not detect the common threads among people who tend to have side effects.
Benefits and drawbacks of intention-to-treat analysis
Intention-to-treat analysis is considered the benchmark in Food and Drug Administration (FDA) applications for new drugs. The pharmaceutical and biotech industries rely on them heavily for approvals of new medications and medical devices.
This analysis type looks at entire data sets without removing anyone from the groups, so it can reveal unexpected or unintended results. That can be helpful when you're trying to determine whether a drug is safe.