Identifying citation classics in the field is one of the key methodologies used to conduct a systematic evaluation of research performance. The objective of this study was to determine the most frequently cited articles published in journals that are placed under the 'respiratory system' subject category (Institute for Scientific Information (ISI) Journal Citation Reports) and to compare them with the most frequently cited respiratory-related articles published in any journal, regardless of subject category. The authors utilized the ISI Journal Citation Reports: Science Edition 2010 database in April 2012 to determine the most frequently cited articles by respiratory system subject category and by respiratory-related keywords. The top 50 most-cited articles were identified in each category and evaluated according to various characteristics. The majority of these papers originated from the United States. The median numbers of citations for the top 50 cited articles stratified by respiratory system subject category and respiratory-related keywords were 841.5 and 2701, respectively. Half of the top 50 cited articles identified by respiratory-related keywords were published in general medical or basic science journals, whereas only three out of these were published in journals under the respiratory system subject category in ISI Journal Citation Reports. In summary, respiratory-related articles published in general medical or science journals attracted more citations than those published in the specific respiratory journals.