As bibliographical classification of published journal items affects the denominator in this equation, we investigated how the numerator and denominator of the impact factor (IF) equation were generated for representative journals in two categories of the Journal Citation Reports (JCR). We performed a full text search of the 1st-ranked journal in 2004 JCR category “Medicine, General and Internal” (New England Journal of Medicine, NEJM, IF = 38.570) and 61st-ranked journal (Croatian Medical Journal, CMJ, IF = 0.690), 1st-ranked journal in category “Multidisciplinary Sciences” (Nature, IF = 32.182) and journal with a relative rank of CMJ (Anais da Academia Brasileira de Ciencias, AABC, IF = 0.435). Large journals published more items categorized by Web of Science (WoS) as non-research items (editorial material, letters, news, book reviews, bibliographical items, or corrections): 63% out of total 5,193 items in Nature and 81% out of 3,540 items in NEJM, compared with 31% out of 283 items in CMJ and only 2 (2%) out of 126 items in AABC. Some items classified by WoS as non-original contained original research data (9.5% in Nature, 7.2% in NEJM, 13.7% in CMJ and none in AABC). These items received a significant number of citations: 6.9% of total citations in Nature, 14.7% in NEJM and 18.5% in CMJ. IF decreased for all journals when only items presenting original research and citations to them were used for IF calculation. Regardless of the journal’s size or discipline, publication of non-original research and its classification by the bibliographical database have an effect on both numerator and denominator of the IF equation.