When Caenorhabditis elegans encounters harsh environmental conditions, it enters a non-aging diapause (dauer), an alternative larval stage capable of long-term survival. This replaces the stage of normal development critical for development of the reproductive organs. Here, we report that increased duration of diapause causes a delay in post-dauer development, and also causes severe defects in the reproductive development of males and hermaphrodites. Thus, the dauer state, while allowing for survival under adverse conditions, has important developmental and reproductive consequences. This effect is more pronounced in males, possibly accounting for the increased survival of C. elegans hermaphrodites in challenging environmental conditions.