Persistence and extinction are key processes in infectious disease dynamics that, due to incomplete reporting, cannot be directly observed. For fully-immunizing diseases, reporting probabilities can be estimated from demographic records and case reports. Yet reporting probabilities are not sufficient to unambiguously reconstruct disease incidence from case reports. Here, we focus on disease presence (i.e., non-zero incidence), which provides an upper bound on disease extinction. We examine measles and pertussis in pre-vaccine era U.S. cities, and describe a conserved scaling relationship between population size, reporting rate, and observed presence (i.e., non-zero case reports). Using this relationship, we estimate disease presence given perfect reporting, and define cryptic presence as the difference between observed and estimated presence. We estimate that, in early 20th century U.S. cities, pertussis presence was higher than measles presence across a range of population sizes, and that cryptic presence was common in small cities with imperfect reporting. Our results suggest that unobserved, cryptic incidence deserves careful attention, particularly in “colonizer” diseases with longer infectious periods and lower transmission rates. Indeed, cryptic presence could paradoxically increase in response to control measures such as vaccination campaigns.