We aimed to assess publication speed of manuscripts submitted to general medical journals and to explore the link with various author, paper and journal characteristics. In this retrospective study of bibliometric data we retrieved 45 randomly selected papers published in 2016 from each of the highest impact factor journals of general internal medicine (n = 9) and primary care (n = 9). Only journals reporting submission and publication dates were included. The following data were extracted: first author (gender, place of affiliation, number of publications), paper (submission and publication dates, online publication, open access, number of authors, number of participants, study design, study results) and journal characteristics (impact factor, number of papers published). We computed for each paper the submission-to-acceptance, acceptance-to-publication and submission-to-publication times. We performed linear regression with random effects models to identify the associations with predictors, adjusting for intra-cluster correlations. A total of 781 papers were included. The overall median submission-to-acceptance time was 123 days (interquartile range 111, min 1, max 922), acceptance-to-publication time 68 days (interquartile range 88, min 2, max 802) and submission-to-publication time 224 days (interquartile range 156, min 24, max 1034). In multivariate analysis, online publication was strongly associated with reduced submission-to-publication time (difference: − 93 days, p value < 0.001). This study provides insight into the submission-to-acceptance, acceptance-to-publication and submission-to-publication times in general medical journals. Researchers interested in reducing publication delays should focus on journals with online publication.