Caffeine has long been suspect of causing mal-formations in fetus, and that it may reduce fertility rates.
These reports have proved controversial. What is known is that caffeine does causes malformations in rats, when ingested at rates comparable to 70 cups a day for humans. Many other species respond equally to such large amounts of caffeine.
Data is scant, as experimentation on humans is not feasible. In any case moderation in caffeine ingestion seems to be a prudent course for pregnant women. Recent references are Pastore and Savitz, Case-control study of caffeinated beverages and preterm delivery. American Journal of Epidemiology, Jan 1995.
A recent study found a weak link between Sudden-Infant-Death-Syndrome (SIDS) and caffeine consumption by the mother, which reinforces the recommendation for moderation -possibly even abstinence- above.
On men, it has been shown that caffeine reduces rates of sperm motility which may account for some findings of reduced fertility.