A light plane pilot took off from 3SQ on a runway he was not cleared to depart from. The reporter alleges the airport runway markings are 'almost nonexistent.'

Narrative

I filed an IFR flight plan and received a weather briefing from Flight Service. I tried to receive my IFR clearance on the frequency listed on the approach plate for St. Charles Municipal Airport (3SQ); which was listed as 120.15. Nobody answered on the frequency after several attempts to make contact. I then called Flight Service on the phone to receive my IFR clearance and was successful in obtaining my clearance. During the clearance request; I was asked which runway I will be departing from. I responded that I will be departing from Runway 9. This was incorrectly stated by myself. The traffic flow was departing/arriving on Runway 27 at 3SQ. I proceeded to taxi and complete my engine run-up and readied myself for departure. I departed Runway 27 from 3SQ. The takeoff proceeded normally and I contacted departure control during the climbout; still in VFR conditions. When I contacted departure control; they asked me which runway I departed from; and I responded that I departed from Runway 27. The Controller informed me that my clearance was to depart from Runway 9; and that I need to stay with the runway that I requested in my original clearance request. The rest of the flight went uneventful. I practiced 4 additional instrument approaches before I returned to 3SQ. The runway markings at 3SQ are almost nonexistent. Controllers monitoring the frequency for clearance delivery as published would be helpful.