Infant mortality is an important population health statistic that is often used to make health policy decisions. For a small population, an infant mortality rate is subject to high levels of uncertainty and may not indicate the “underlying” mortality regime affecting the population. This situation leads some agencies to either not report infant mortality for these populations or report infant mortality aggregated over space, time or both. A method is presented for estimating “underlying” infant mortality rates that reflect the intrinsic mortality regimes of small populations. The method is described and illustrated in a case study by estimating IMRs for the 15 counties in California where zero infant deaths are reported at the county level for the period 2009–2011. We know that among these 15 counties there are 50 infant deaths reported at the state level but not for the counties in which they occurred. The method’s validity is tested using a synthetic population in the form of a simulated data set generated from a model life table infant mortality rate, representing Level 23 of the West Family Model Life Table for both sexes. The test indicates that the method is capable of producing estimates that represent underlying rates. In this regard, the method described here may assist in the generation of information about the health status of small populations.