I checked my nest box, and found dead babies. Why?

Several factors can lead to this situation. Parents may abandon a nest for several reasons. Species competing for a nest box may usurp a cavity with an active nest. The non-native House Sparrow (Passer domesticus) is infamous for killing nestlings and occasionally an adult bird. Severe parasite infestations could render the young so weak they cannot survive. Starvation could occur under several situations, such as limited food availability due to cold weather or if one parent disappears during the nestling stage. (Though one parent can sometimes make up for the for the loss by increasing their feeding rate.)

Other causes of death include genetic disorders and chemical poisoning which are both difficult to diagnose without lab analysis. Nests are sometimes deserted by parents as a result of natural causes such as inclement weather, limited food resources, or death of a parent. If one parent disappears, the remaining parent may abandon the nest, search for a new mate and start over. A competing individual may drive them off of their territory, or a competing species may usurp their nest site.