Risks for selected congenital anomalies from parental smoking were investigated in a case-control study in California. Mothers of 207 infants with conotruncal heart defects, 264 infants with neural tube defects, 178 infants with limb deficiencies, and 481 live born control infants delivered in 1987-1988 were interviewed by telephone. Modestly elevated risks were observed for conotruncal heart defects and limb deficiencies, associated primarily with both parents smoking. An odds ratio of 1.9 (95 percent confidence interval 1.2-3.1) was observed for conotruncal heart defects and an odds ratio of 1.7 (95% confidence interval 0.96-2.9) for limb deficiencies when both parents smoked compared to neither parent smoking. We did not observe increased risks associated with maternal smoking in the absence of paternal smoking, although an increased risk associated with paternal smoking in the absence of maternal smoking was observed for limb deficiencies in offspring. For conotruncal defects, the risks associated with parental smoking differed among race/ethnic groups. Parental smoking was not associated with increased risks for neural tube defects. Observed risks did not change substantially when adjusted for maternal vitamin use, alcohol use, and gravidity. Some heterogeneity in risk was observed for phenotypic case subgroups, but data were too sparse to draw firm inferences.