Health information systems are essential to ensure the safety and quality of health care and improve adherence to clinical practice guidelines, but they are also a very powerful tool concerning resources management and control, decision making, and effective and efficient planning of prevention and control interventions [
1,
2]. However, the incompleteness and inaccuracy of the information is common in this type of registries and can lead to problems at a clinical level, but also at a population level such as the underestimation of some diseases. In Catalunya (Spain), the Information System for Research in Primary Care (SIDIAP) was launched in 2010 with the integration of data from the clinical work station of primary care (ECAP) of the Catalan Health Institute (ICS), which started in 1998, and other complementary sources [
3]. The ICS is the main provider of health services in Catalunya and manages 283 out of 370 Primary Care Teams with a catchment of 5,564,292 people, approximately 74% of the Catalan population (
http://ics.gencat.cat/es/lics/). Nevertheless, it is reasonable to assume that the incidence of genital warts (GW) will be very similar among the Catalan population not covered by ICS. In the particular case of sexually transmitted diseases, it is even more important to have reliable information due to their remarkable morbidity, and therefore, the importance of controlling trends over time and priority setting (see [
4] for a comprehensive discussion focused on developing countries). GW are a common and highly contagious sexually transmitted disease in Catalunya (in 2016 the incidence was about 107 cases per 100,000 women and 139 cases per 100,000 men[
5]) caused by a subset of HPV types, with the most common being genotypes 6 and 11. They are usually benign, or non-cancerous, skin growths that develop on the genital area. However, they have an important negative impact on the health service and the individual, in addition to have a large economic burden and affect several aspects of quality of life [
6‐
8]. A higher risk of CIN2+ lesions in women following a GW diagnose has been reported in a comprehensive recent study, even more than four years after the GW diagnose [
9]. It is well known that incidence data underestimate, to some degree, the real occurrence of genital warts because this infection is often under-reported, mostly due to their specific characteristics such as the asymptomatic course of the disease [
10]. This issue might be even more severe in specific vulnerable populations as imprisoned women [
11]. Further, the SIDIAP database only includes data from the public healthcare sector and around 28% of the general population in Catalunya have a double health insurance coverage, public and private, so this fact can also explain why GW incidence rates are underestimated [
12], although this source of under-reporting cannot be detected by the proposed model as we only have data from the public health system. There has been a growing interest in the past recent years to deal with data that are only partially registered or under-reported in the biomedical literature [
13‐
18]. Most of these previous works deal with discrete-valued time series, whereas this paper is focused on the incidence of a disease, which should be treated as a continuous-valued time series. Therefore, the aim of this work is to quantify the under-reporting of genital warts cases in Catalunya and the reconstruction of the actual incidence in the period 2009-2016 on the basis of the mixture model described in the next Section.