An epidemic of dengue during 2001 in Northwestern Peru reemphasized the need for efficient, accurate, and economical vector surveillance. Between November 1998 and January 1999, we carried out extensive entomological surveys in two neighborhoods of ≈600 contiguous houses located in the Amazonian city of Iquitos, providing a unique opportunity to evaluate the Aedes aegypti (L.) rapid assessment survey strategy. Based on Pan American Health Organization recommendations, this strategy is used by the Peruvian Ministry of Health (MOH). In our analysis all household locations, including closed and unoccupied houses, were georeferenced and displayed in a geographic information system, which facilitated simulations of MOH surveys based on hypothetical systematic sampling transects. Larval, pupal, and adult mosquito indices were calculated for each simulation (n = 10) and compared with the indices calculated from the complete data set (n = 4). The range of indices calculated from simulations was moderately high, but included actual indices. For example, simulation ranges for house indices (HI, percentage of infested houses from complete survey) were 38–56% (45%), 36–42% (38%), 21–34% (30%), and 13–33% (27%) in four surveys. HI, Breteau index, pupae per hectare, adult index, and adults per hectare were more robust entomological indicators (coefficient of variation [CV]/mean = 0.1–2.9) than the container index, pupae per person, pupae per house, adults per person, and adults per house (CV/mean >20). Our results demonstrate that the MOH’s Ae. aegypti risk assessment program provides reasonable estimates of indices based on samples from every house. However, it is critical that future studies investigate the association of these indices with rates of virus transmission to determine whether sampling variability will negatively impact the application of indices in a public health context.