It is a natural attribute to feel guilty when we do something that is harmful for us.  This is a self survival mechanism created to help us navigate this life of land mines that can totally destroy our life.  The Bible makes it clear that the purpose is for our own protection.  Ultimately if we decide to go against our guilty feelings we will suffer the consequence up to death.  The conscience can be used as a guide to help us walk in a safe manner as we navigate this life or it can become an enemy that constantly strives against our desires that we may have given into.
Depending on what your decision has been you will either condemn your actions in your conscience and respond accordingly or you will excuse your actions in your conscience and try to ignore the nagging guilt or rationalize it away.  Regardless of the decision, all men must deal with the inner man called the conscience.
From the earliest days of our lives we can remember that we were told not to run into the street, don't play with knives, fire, and later on don't have sex outside of marriage, don't take drugs, don't drink alcohol, etc.  All of these rules were really just warnings from our parents or caregivers that were intended to keep us from harm.  Since we were so young we did not know the dangers that awaited us in the world.  We needed someone who had already been down the path and experienced the pain brought on by ignoring these warnings to enlighten us.  It was our decision to believe our parents/caregivers and heed the warnings or ignore the warnings and check it out for ourselves.  Obviously everyone has checked it out themselves many times in their lives and found validity in the warnings of their childhood.  It was never necessary for us to be taught how to ignore these warnings.  It was natural for us to want to give into them.  So then the conscience is meant to convict us of our actions so that we will change them to survive.  Much in the same way that a toddler responds when he first begins to walk.  At first he manages to pull himself up on something like the sofa and begins his balancing act for the first time.  After a very short time, he loses his balance and falls to the floor.  This may create quite a bit of pain until he learns to put out his arm to buffer the landing.  The pain he may feel when he hits the floor will be a staunch reminder that the action he just took has a consequence called pain.  This is the way our bodies teach us that not all actions are good for us.  This consequence however, is minor as nature softly begins life's lessons.  As we grow we are presented with many, many more opportunities to play chicken with the consequences.  We have the same decisions to make that we started out with as a child, such as whether to believe those that deliver the warnings or ignore them.  Regardless of your personal religious beliefs, you will constantly face these decisions in your life.  Do not speed, Do not get drunk in public, do not drink and drive, don't be late to work, do not harm others.  Whatever the warning, there is a consequence to it if disobeyed.  The bible says that the punishment of God resides on the disobedient.  Put plainly, there is a consequence for every action that violates God’s natural design.  It matters not if you choose to disbelieve His warning.  
Three men are standing on a 15,000 foot cliff that towers above a bed of sharp jagged rocks.  One is a Christian.  One is a Muslim and one is an atheist.  Which one will survive if they all three jump off?  Exactly, none of them because they all broke the natural law of gravity.  It is much the same with all of God’s laws be they physical laws, dietary laws, sexual laws, etc.  Even a Christian will pay the natural consequence of His actions while he is on this planet.  It does not matter if you are a Christian or unbeliever, if you violate God’s dietary laws you will pay a consequence in your body in the form of sickness.  
Paul stated in scripture that he always strove to have a clear conscience before God.  Acts 23:1 (KJV)
And Paul, earnestly beholding the council, said, Men and brethren, I have lived in all good conscience before God until this day.
Acts 24:16 (KJV)
And herein do I exercise myself, to have always a conscience void of offence toward God, and toward men.
He knew that would be profitable for him, for God and for those who heard him. That is part of trusting God and taking Him at His word.  If we have a clear conscience we can know that we are being honest with ourselves and with God.  This is what the Lord requires from us, truth in the inward parts.
Psalms 51:6 (KJV)
Behold, thou desirest truth in the inward parts: and in the hidden part thou shalt make me to know wisdom.
In conclusion;  our conscience is our spiritual GPS (God Positioning Satellite) that communicates with God to give us direction in our life.  If we have this GPS turned on, we can walk through life with confidence and a clear conscience communicating with the Lord continuously and avoiding many consequences but if our GPS does not work, we are in for a life of torment and ultimate destruction.
How does one turn this GPS on?  By trusting in Christ Jesus alone.  He is the Way, The Truth and the Life and only by following Him can we have hope in this life and the life to come.  Romans 10:9-13


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