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Over the years I have travelled from Canada to the USA and back again many times. Below, I've detailed the steps for successfully crossing the border with as little stress as possible.
 
Travelling with horses, accross the border from Canada to the USA: TEMPORARY
 
1) Have your vet come out to do your health papers for temporary residency, a current coggins is needed for this
2) Your health papers will need to be stamped by the Canadian Food Inpection Angency. Your vet may be able to have this done for you for a fee. It costs $15 (as of 2015) at the CFIA. You can find a list on the CFIA website of the Animal Health Offices. They generally keep standard business hours and close for an hour at lunch. Make sure you make a bunch of copies of the stamped health papers.
3) I generally use the Queenston/Lewiston bridge, as that is closest to where I live, but I believe any crossing is appropriate on temporary papers.
4) When entering into the states, you can stay in the auto/RV lanes (assuming you are using a pickup truck and trailer, not a transport).
5) When you arrive at the border, you will have to hand over a copy of the health papers, and your passport. You will then be instructed to go inside the immigration area where a US border official will review the health papers and issue you a stamped document that shows the horse(s) have entered the states. This will have to be restamped on your exit from the states.
6) On your way back from the states, you will again have to stop at the immigration area stateside, to have the document stamped approving that you are leaving the country with the horse(s).
7) To cross into Canada, use the commercial (truck) lanes, not the auto/RV. All you need to do once you arrive at the window is hand over a copy of your temporary papers, show your passport, and make any declarations.

 

Travelling with horses, accross the border from Canada to the USA: PERMANENT
 
1) Have your vet come out to do your health papers for permenant residency, a current coggins is needed for this
2) Your health papers will need to be stamped by the Canadian Food Inpection Angency. Your vet may be able to have this done for you for a fee. It costs $15 (as of 2015) at the CFIA. You can find a list on the CFIA website of the Animal Health Offices. They generally keep standard business hours and close for an hour at lunch. Make sure you make a bunch of copies of the stamped health papers.
3) You must cross at a border that has a designated veterinarian. This is the Lewiston/Queenston bridge for me.
4) When entering into the states, you can stay in the auto/RV lanes (assuming you are using a pickup truck and trailer, not a transport).
5) When you arrive at the border, you will have to hand over a copy of the health papers, and your passport. You will then be instructed to go inside the immigration area.
You will be asked a lot of questions your first time through. Be prepared to show proof of where you and the horse will be staying, proof of appropraite health insurance, proof of where you work, and proof that you have a job/obligations to come back to in Canada. The border agents can be tough!!
If you have successfully navigated questioning to this point, the border agents will give you a stamped paper which you will need to take down the road to the vet office.
6) Now you must drive down the road to visit the US vet inspection. This office has standard business hours (not open on weekends) and closed an hour at lunch. It is mandatory to stop so ensure you plan your route so you can get to the vet while they are open!
7) To get back into Canada you will need a vet to fill out a new set of health papers.
8) To cross into Canada, use the commercial (truck) lanes, not the auto/RV. All you need to do once you arrive at the window is hand over a copy of your temporary papers, show your passport, and make any declarations.

 

Caledon, Ontario, Canada;   Cell: (519) 777-0875   email: liz_hawley@yahoo.ca