This study proposes a methodology for estimating the hidden criminal population working in markets of drug trafficking, prostitution exploitation and smuggling in Italy during the period 2006–2014. These estimates represent the first step of a wide procedure that has the final objective of measuring the economic flows of illegal transactions in national accounts. We exploit administrative registers coming from the Ministry of Justice, and consider these registers as lists of potential criminals. Unique codes for denounced criminals are not available, limiting so far its exploitation at micro level. This drawback has been overcome in this work by proposing an adjustment of the Zelterman estimator that accounts for the potential linkage errors caused by the lack of exact unique identifiers in the dataset. We obtain yearly estimates of the population size of criminals including also the unknown population, for the crimes of drug trafficking, prostitution exploitation and smuggling during the period 2006–2014.