Do I have to pass through customs in Canda if I am just making a connecting flight?

Depends, which airport??? Also is connecting flight into Canada or Int'l? Larger airports have facility to allow connection for Int'l flight without customs, however some do not and yes you go thru customs and then try to make your connection. Mirabel - supposed to have connection faciltation, Dorval (Trudeau airport) used to have (I believe limited) Pearson (toronto) is supposed to have connect facilitation (especially since all the new construction), Hamilton go thru customs (unless they changed). So it goes across the country. Best idea is consult with your air carrier, as they should have this information available.