by 
The Curious Bag
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A check engine light indicates there is a malfunction related to the emission control system. This is different from other indicator lights, such as low fuel, and concerns only vehicle emissions. If this light is continuously on, there is a problem that may warrant service.
Misfire Condition
If the light is continuously turning on and off, it likely means the engine is misfiring. The misfire could increase vehicle emissions and damage the vehicle if not corrected.
Fuel Cap
The On-Board Diagnostics system can determine if the fuel cap is loose, missing or improperly installed, which can increase emissions because fuel evaporates into the atmosphere.
Wet Electrical System
Driving through deep puddles of water can contribute to a wet electrical system. It should self-correct once the system dries out.
Poor Fuel Quality
Poor quality fuel may cause stalling, misfiring or hesitation on acceleration. Using one full tank with a good quality fuel should fix the problem.
Electronic Throttle Control System
There may be a problem with the electronic throttle control system if the engine speed does not increase when you accelerate. You may still be able to drive at low speeds, but the vehicle should be checked.
Source:
2004 Owner's Manual: Toyota 4Runner
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