I.L.
My daughter was very sick as an infant. In the first two years of her life she was in the hospital and doctors office dozens of times. Many times the procedures were not pleasant. She was so afraid of the doctor at this age, that just walking into the lobby of the office she would start shaking, her whole body trembled.
Around age three it ended. I remember the first time we went that she did very well. She had bronchitis and was feeling miserable. We did lots of pep talks about how the doctor can help her feel better. She was nervous at the doctor but did not freak out like she normally did. When it was over and she saw that nothing hurt she was fine. We made a VERY big deal throughout and afterwards about what a good job she did. She is five now and is a champ at the doctor.
Some tips:
The berenstein bears and little critters have a book about going to the doctor. I recommend getting these and any other kids books you can find and reading them regularly (not just before a doctor trip).
On trips that you go to the doctor for you and he is with you, talk to him before and during. Let him know where you are going and that it is for you. I remember several occasions I would tell my daughter we were going to the doctor for mommy and her asking me over and over "I no see doctor, mama see doctor. right mama?" She did fine then, but she also got to see that the doctor was not hurting mama.
Talk about going to the doctor and how they help people feel better.
Do not make any big deal out of going, and if he throws a fit comfort him but do not be overly attentive or at all emotional with him.
If he is good waiting in the lobby give him lots of praise. If he is good waiting in the exam room give him lots of praise. He won't be comfortable with the doctor if he already has himself worked up in the lobby!
Lastly, just be patient. Chances are he will grow out of this.