The only problem with Julie and Anni's answer is that they are just guesses -- for good or bad, the only real answer to your question, Anna, is "we don't know because the show never gave any information at all about what the problem was." As LauraA says, it's up to each fanfic writer to determine that for themselves.
I think LauraA sums it up very well, though -- writers might take the stance that it's impossible for them to conceive or that Clark has a solvable fertility problem that has nothing to do with his alien orgins. Or they might decide they will have no fertility problems at all.
This second scenario is the one we took in Season 5. We gave Clark a relatively common male fertility problem, but with a twist -- being an alien, it turned out that he had a "cycle" just like a human female would, and would thus test fertile only at periodic intervals. The trick for L&C, then, was to match their fertility cycles so they could conceive. (This solution had the added benefit of explaining why Dr. Klein would decide Superman was infertile, while Sam Lane, testing several weeks later, would see no problem.)
So bottom line: It's up to you as the fanfic writer to decide how you want to handle the situation.
Oh, but for the record, although they never identified Clark's exact problem on the show, we do know from the writers that Dr. Klein would have ultimately been proven wrong. The baby from "Family Hour" was intended to be a decendent of theirs from the future, and finding this out (presumably in the 5th season premiere) would have given L&C the knowledge that someday they would conceive. In this case, Sam Lane was right when he looked at Dr. Klein's data and said "this isn't right" -- he just got his memory wiped before he could tell L&C what he'd found.
Kathy
