Abstract Introduction Health care information systems can generate and/or record huge volumes of data, some of which may be reused for research, clinical trials, or teaching. However, these databases can be affected by data quality problems; hence, an important step in the data reuse process consists in detecting and rectifying these issues. With a view to facilitating the assessment of data quality, we developed a taxonomy of data quality problems in operational databases. Material We searched the literature for publications that mentioned “data quality problems,” “data quality taxonomy,” “data quality assessment,” or “dirty data.” The publications were then reviewed, compared, summarized, and structured using a bottom-up approach, to provide an operational taxonomy of data quality problems. The latter were illustrated with fictional examples (though based on reality) from clinical databases. Results Twelve publications were selected, and 286 instances of data quality problems were identified and were classified according to six distinct levels of granularity. We used the classification defined by Oliveira et al to structure our taxonomy. The extracted items were grouped into 53 data quality problems. Discussion This taxonomy facilitated the systematic assessment of data quality in databases by presenting the data's quality according to their granularity. The definition of this taxonomy is the first step in the data cleaning process. The subsequent steps include the definition of associated quality assessment methods and data cleaning methods. Conclusion Our new taxonomy enabled the classification and illustration of 53 data quality problems found in hospital databases.