BACKGROUND: The number of shots in the childhood immunization schedule has been increasing and is likely to continue to increase in the coming years. Consideration of the psychologic costs of multiple injections, adverse events and vaccine-preventable disease is therefore growing in importance. METHODS: We assessed parent preferences, using both the time tradeoff (i.e. amount of parent time willing to trade) and willingness-to-pay (i.e. dollars willing to pay) metrics, for possible outcomes of vaccination among 206 parents of infants receiving care at Kaiser, Northern California Region. We also explored the relationship between preferences and subject characteristics. RESULTS: In general the amount of time subjects were willing to give up and the quantity of money they were willing to spend to avoid an outcome increased with the severity of the outcome. Preferences for our six main outcomes of interest all differed from one another (P < 0.0001, Tukey's multiple comparisons procedure). Rank correlation coefficients between time tradeoff and willingness-to-pay values for the six main outcomes ranged from 0.42 to 0.52 (all P < 0.004). Subject characteristics, including education, income, race/ethnicity and the child's birth order, did not explain the variation in parent preferences. CONCLUSIONS: In general subjects were willing to give up more money or time to avoid less desired outcomes. They were willing to give up only very small amounts of their own life expectancy or money to avoid minor, temporary outcomes (e.g. moderate fussiness, fever and pain) whereas they were willing to forego substantial lengths of their life or amounts of money to avoid a major, permanent outcome (i.e. permanent disability). Nonetheless much variation surfaced in the amount of time (or money) subjects were willing to trade to avoid outcomes. If this variation represents true differences in preferences, guideline developers must consider the role of individual parent preferences in decisions concerning vaccination.