According to the web site links below, it will degrade with chloroform. The tests assume 100% chloroform, the vials will probably be fine with dilute chloroform for at least a short time. The best thing to do is to test a vial with the solution you will use (containing no sample) to verify that it will work at the concentration you will use.

http://www.plasticsintl.com/plastics_chemical_resistence_chart.html

http://www.coleparmer.com/Chemical-Resistance

Halogenated hydrocarbons may not be compatible with polycarbonate  . For this reason we are using glass vials for centrifuging the sample of lipid extracts. 

I agree with Abdur, you should use glass tubes for the lipid extraction

Thank you very much for your answers!:)

This answer is maybe a little bit late but it's better to use glass when there is chloroform in your extraction fluid. I started to use polycarbonate-vails and in the beginning it was no problem but after several extractions there were problems with the samples. The problem was solved by using glass material so it's better to avoid polycarbonate material.