Side effects are negative effects imparted by ingredients. These range from causing headaches to permanent paralysis, but are universally effects that are not wanted in a finished drug. Releasing a drug with active side effects will have a negative impact on sales and clinical trial results, further depressing sales.
It is also important to note that catalysts are always part of a side effect, not a cure effect. In the example, we can see "Encourages Anxiety" is a Type 2 catalyst, while "Urinary Retention" is a Type 3 catalyst. When making a drug whose cure requires upgrades, if the upgrade requires a catalyst, the appropriate one will need to be present for processing. Often, this means adding a side effect - sometimes a very bad one - to the drug during processing in order to enable the cure upgrade. This is not necessarily a permanent problem, however, as side effects can be removed prior to packaging and sale of the drug. When attempting to maximize sales and reputation, doing so is highly recommended.
Note that not all side effects are created equal; some, like "Permanent Paralysis", would have a much worse effect on your cure rating than something like "Induces Sleepiness". Generally, the more dots a catalyst has, the worse the side effect is considered to be, while the side effects without catalysts are considered the most minor.
Processing machinery is blind to whether a particular effect is a cure or side effect; they are all affected equally. This means that passing a drug with side effects through a Hadron Collider will maximize the negative results of the side effects while it maximizes the positive effect(s) of the cure(s) present.
Before sending a drug for packaging, all side effects should either be inactivated or, if that isn't possible, removed. Side effects can be inactivated by ensuring that the drug's final concentration is outside the side effect's spectrum of activity. However, as side effects often have a wide activity spectrum, the cure's effective and/or maximum concentration will typically overlap with at least one side effect's activity spectrum, leaving the drug with a side effect. In this case, the answer is to remove the side effect from the compound. Despite what some side effects would seem to indicate, all side effects can be removed from a drug.
When a side effect is removed from a drug, it leaves behind an empty slot in the position it once held. This is particularly important when blending ingredients in a multimixer, as effects can only be added to a base ingredient with empty slots.
Removable effectsSide effects that can be removed will show the conditions necessary to remove it when mousing-over the side effect. In the example shown at right, the Blurs Vision side effect is removable; the information panel titled Remove shows how to do so. Effectively, removing a removable side effect is the same as upgrading a cure that requires no catalysts: the concentration must be adjusted to the specified level, then the listed processing machine must be used. As with upgrading a cure, when the correct concentration is achieved to allow the side effect to be removed, a green check mark will appear next to the "conc." pre-requirement.
In the example shown to the right, the concentration must first be lowered to between zero and three. Once this is done, passing the compound through an agglomerator will remove the side effect.
Mousing over a side effect may show a "Cannot Remove" tab rather than the removal requirements box. This means that the side effect cannot be deleted through normal processing methods. However, the side effect can still be removed by replacing it. You may mix your drug into another ingredient using the Multimixer (but you must choose the other ingredient as the base, and have the slot open for your cure), or you may swap the side effect onto another ingredient using the Centrifuge.
If you have the Marketing and Malpractice DLC, you can also use the Booster Mixer to replace a side effect. To do so, a booster must be used. First, a second ingredient must be imported, and it must have a booster effect. Using a Shaker, the booster must be positioned in the same slot in that ingredient as the unremovable side effect in the base ingredient. Finally, the base and booster ingredients are fed into a Booster Mixer, where the booster effect overrides and replaces the existing unremovable side effect.