A therapeutic effect is a consequence of a medical treatment of any kind, the results of which are judged to be desirable and beneficial. This is true whether the result was expected, unexpected, or even an unintended consequence of the treatment. An adverse effect, on the other hand, is a harmful and undesired effect.
What constitutes a therapeutic effect versus a side effect is a matter of both the nature of the situation in which a treatment is used and the goals of treatment. There is no inherent difference between therapeutic and undesired side effects; both responses are behavioral/physiologic changes which occur as a response to the treatment strategy or agent. The most common nominal reason for preferring certain effects is avoiding death. However, those changes which are viewed as desirable, given the situation, are called therapeutic; those undesirable for the situation are viewed as harmful.
Scope of treatments 
Many people think of therapeutic and undesired side effects as only applying to medications, drugs or supplements, perhaps because pharmacology approaches are more often more rigorously evaluated by carefully controlled comparisons with placebo treatments, but this is not the case. It applies to any treatment approach, including surgery, physical therapy, psychotherapy, treatment with compounds, faith healing, hypnosis, holistic methods, etc.; any method of which one can conceive.
The administration of a compound was selected for the pharmacologic example below because this form of treatment is often more readily evaluated by comparison with a placebo approach; the comparison designed so that people are unable to recognized the difference, at least at a conscious or group awareness level. Other therapeutic methods are typically more difficult to test because the test subjects can more easily recognize the key aspect of treatment which is being tested; it thus becomes far more difficult to apply the placebo control methodology. The placebo effect is always relevant in all treatments; behavior and symptoms do change, however the presumed mechanism may primarily be the power of the mind which controls behavior and perception all the time, and the fact that if an individual believes that their situation will change then their situation actually does change.
To maximize the therapeutic effects and minimize the side effects of any treatment, recognition and quantification of the situation, in multiple dimensions, is a critical prerequisite. There are many situations in which the effects of a treatment, both those often viewed as both desirable and undesirable can be used in combination with other treatments in a complex strategy so that, for the individual being treated, the best end results actually depend on side effects contributing to the overall therapeutic benefit. Achieving this reflects a higher degree of physician and patient interactive relationship, trust, sophistication and skill. The same principles applies to all agents, including what most people view as simply food, water, air and oxygen. Situation, timing and great familiarity of the multiple usual responses to agents is critically important for wisely selecting all treatments. Maintaining and improving health strongly depends on promoting desirable effects while lessening the impact of undesirable effects of many interacting issues. However, the number of interacting issues, powerfully influenced by internal individual control mechanisms, make understanding and knowing all the issues a mind-boggling complex task which, at least in this day and age, is never totally understandable. There are simply too many complex interacting issues, never totally knowable, definable and predictable.
Pharmacology example 
For example, it is widely promoted that "natural" or "organic" agents are more healthy. However, everything in the world has multiple and varying responses when used; both desirable and undesirable effects are inherent parts of the total response. Even water – on which all life on earth depends – can have undesirable, even fatal effects; while increased intake of water can save a dehydrated patient, too much water can lead to water intoxication, which can result in death, such as in severe pulmonary edema.
As a simple example, the therapeutic effect of diphenhydramine, when used for nasal congestion, is to lessen mucous membrane secretions and the side effect is drowsiness. However, when used for insomnia, as in many over-the-counter preparations, the therapeutic effect of diphenhydramine is drowsiness and the side effect is mucous membrane dryness, which is undesirable, especially if the person using the agent for sleep is already suffering from dry membranes. The more important issue is not the agent, but the situation in which the therapeutic agent is used; a change in the situation can easily totally reverse what is usually considered a therapeutic versus an undesirable side effect.
Diphenhydramine was originally marketed under the brand name Benadryl in the early 1950s. When taken orally, it typically induces two behavioral responses: (1) drying of mucous membranes, potentially helpful in cases of increased nasal congestion and (2) drowsiness. Diphenhydramine was promoted for reducing nasal congestion, thus response 1 was the considered the therapeutic effect. Since response 2, the drowsiness response, was typically not viewed as desirable, drowsiness was termed a side effect.
When diphenhydramine is used as a treatment, these two effects, individual responses, are always bound together and cannot be separated. Even though the dose can be changed and the relative degree of the two responses may be reduced or increased and the degree of the two different responses may be somewhat different at different doses, the two responses cannot be separated. For simplicity of illustration, only two typical responses are mentioned. For completeness, be aware that as with most treatments people usually exhibit additional responses to diphenhydramine beyond the two mentioned.
Reducing complexity 
The desire to simplify clinical situations and variables is one of the important reasons that physicians often prefer highly refined and regulated prescription drug preparations, as opposed to less refined and regulated products, often marketed as "natural" to imply safety.
Products from nature are essentially always complex mixtures of large numbers of different chemical agents, many only partially understood in term of usual desirable and undesirable responses, relationships of these effects to specific doses and with varying amounts of dose present within any given sample available.
The pharmaceutical industry highly purifies, concentrates and sometimes makes very controlled modifications of agents obtained from natural sources, when there is no alternative source, so as to select out and greatly reduce the variables in the treatment agent offered. Ratios of relative responses, often summarized using the concept therapeutic index, are utilized to help understand and communicate treatment responses.
A pharmaceutical grade agent does not make the patient any more simple but it does greatly simplify, narrow and make more definable and predictable both the usual desirable and undesirable effects of the treatment agent, based on careful tracking of the responses of many individuals who have taken the agent, in widely varying amounts and situations, in the past. This purification can greatly improve the probability for both the patient and the physician that the resulting responses to the treatment are likely to be more predictable and controllable.
- "Medline Plus". United States Federal Government National Library of Medicine and the National Intitues of Health.