Oops, prkos and I were typing a response at the same time
The other way is through Fill and Stroke dialogue, choose the Fill tab and there is a button there to remove the Fill.
You could also check the Stroke paint tab. It sounds like you might have the stroke removed. The 2nd button from the left, next to the X will replace the stroke.
If that solves your problem, while the circle is still selected, please go to File menu > Inkscape Preferences > Tools > Shapes > Ellipse > click the option "This tool's own style", and then click the bar that says "Take from selection". Now every time you draw something with the ellipse, it will have the stroke (and whatever color you used for the fill, if you used a fill). Also if this solves your problem, you can do the same for the rectangle, and all the shapes.
Or maybe for some reason

your stroke has been either reduced to 0.00 Width (Stroke style tab, Width should be anything but 0)) or made transparent (Stroke paint tab, at the bottom, Opacity slider should be all the way to right, 100.0). And again, if either of these solves the problem, follow the same procedure I outlined above, to set your shapes' styles, so that you have a stroke every time you use the shape.
Let us know what happens. If still no luck, maybe you could upload an attachment to your next message, an SVG file, so that we can examine it "in person"

, and hopefully find the problem.