I have a problem with one of my .svg files which contains gradients. Indeed, when i convert it in .pdf, gradients are not preserved !
I noticed that when i create the same gradient with Illustrator and then save in .pdf, there is no problem.

Is that a matter of pdf version (1.4 for inkscape vs up to 1.7 in illustrator) ?
Please tell me how to convert well my svg files into pdf ones

You could of course try Apache Batik and see what that does.

Gradients should convert over. There might be another reason why it's not working.

Try creating a new file with an object with a gradient fill and see if that saves ok to PDF.