Birth defects have been the leading cause of infant death in the United States for over the last decade. However, there is little population-based data on the first-year mortality rates for many specific birth defects and the factors that may affect these mortality rates. This investigation examined the first-year mortality rates for 54 selected birth defects of various organ systems in Hawaii during 1986-1999 using data from a population-based birth defects registry and evaluated the impact of the presence of chromosomal abnormalities and other structural birth defects and the year of delivery on the mortality rates. Mortality rates varied widely by defect, being highest for anencephaly (100%), trisomy 13 (82%), and trisomy 18 (74%), while no first-year deaths were reported for glaucoma, bladder exstrophy, and persistent cloaca. The majority (36 of 54 or 67%) of the birth defects had a mortality rate of less than 25%. Among the 51 structural birth defects, 38 (75%) had higher first-year mortality rate for cases with chromosomal abnormalities and 42 (82%) had higher first-year mortality rates for cases with other major structural birth defects. The mortality rate among 1986-1992 deliveries was higher than the mortality rate among 1993-1999 deliveries for 37 (69%) of the 54 birth defects. This study indicates that first-year mortality rates vary widely by type of birth defect, although the mortality rate for the majority of birth defects is relatively low. The presence of a chromosomal abnormality or other structural birth defect increases the mortality rate, and mortality rates for the majority of birth defects have declined in Hawaii during the study period. Copyright 2003 Wiley-Liss, Inc.