Background Presenting to primary care with fatigue is associated with a wide range of conditions, including cancer, although their relative likelihood is unknown. Aim To quantify associations between new-onset fatigue presentation and subsequent diagnosis of various diseases, including cancer. Design and setting Cohort study of patients presenting in English primary care with new-onset fatigue during 2007-2017 (fatigue presenters (FPs)), compared to non-fatigue presenters (NFPs), using Clinical Practice Research Datalink data linked to hospital episodes and national cancer registration data. Method We described excess short-term incidence of 237 diseases in FPs compared to NFPs. We modelled disease-specific 12-month risk by sex and calculated age-adjusted risk. Results We included 304,914 FPs and 423,671 NFPs. 127 of 237 diseases studied were more common in male FPs than in male NFPs, and 151 were more common in female FPs. Diseases that were most strongly associated with fatigue included: depression; insomnia & sleep disturbances, and hypo/hyperthyroidism (women only). By 80 years, cancer was the 3rd most common disease and had the 4th highest absolute excess risk in male FPs (FPs: 7.0%, CI = 6.6 to 7.5; NFPs: 3.4%, CI = 3.1 to 3.7; AER: 3.7%). In women, cancer remained relatively infrequent; by age 80 it had the 13th highest excess risk in FPs. Conclusion Our study ranks the likelihood of possible diagnoses in fatigue presenters, to inform diagnostic guidelines and doctors' decisions. Age-specific findings support recommendations to prioritise cancer investigation in older men with fatigue, but not women.