Despite the centrality of disciplinary classifications in bibliometric analyses, it is not well known how the choice of disciplinary classification influences bibliometric representations of research in the social sciences and humanities (SSH). This is especially crucial when using data from national databases. Therefore, we examine the differences in the disciplinary profile of an article along with the absolute and relative number of articles across disciplines using five disciplinary classifications for journals. We use data on journal articles (2006–2015) from the national bibliographic databases VABB-SHW in Flanders (Belgium) and Cristin in Norway. Our study is based on pairwise comparisons of the local classifications used in these databases, the Web of Science subject categories, the Science-Metrix, and the ERIH PLUS journal classifications. For comparability, all classifications are mapped to the OECD Fields of Research and Development classification. The findings show that the choice of disciplinary classification can lead to over- or underestimation of the absolute number of publications per discipline. In contrast, if the focus is on the relative numbers, the choice of classification has practically no influence. These findings facilitate an informed choice of a disciplinary classification for journals in SSH when using data from national databases.