We described the design of a web-based application (the Software Integrated Cancer Registry—SWInCaRe) used to administer data in a cancer registry and tested its validity and usability. A sample of 11,680 records was considered to compare the manual and automatic procedures. Sensibility and specificity, the Health IT Usability Evaluation Scale, and a cost-efficiency analysis were tested. Several data sources were used to build data packages through text-mining and record linkage algorithms. The automatic procedure showed small yet measurable improvements in both data linkage process and cancer cases estimation. Users perceived the application as useful to improve the time of coding and difficulty of the process: both time and cost-analysis were in favor of the automatic procedure. The web-based application resulted in a useful tool for the cancer registry, but some improvements are necessary to overcome limitations observed and to further automatize the process.