Common skin disorders such as acne vulgaris, rosacea and folliculitis are bothersome prevalent inflammatory diseases of hair follicles that can easily be investigated bedside using optical coherence tomography (OCT) and reflectance confocal microscopy (RCM) with micrometre resolution, opening a novel era for high-resolution hair follicle diagnostics and quantitative treatment evaluation. EMBASE, PubMed and Web of Science were searched until 5 January 2023 to identify all studies imaging hair follicle characteristics by RCM and OCT for diagnosis and monitoring of treatment in hair follicle-based skin disorders. This study followed PRISMA guidelines. After inclusion of articles, methodological quality was assessed using the QUADAS-2 critical appraisal checklist. Thirty-nine in vivo studies (33 RCM and 12 OCT studies) were included. The studies focused on acne vulgaris, rosacea, alopecia areata, hidradenitis suppurativa, folliculitis, folliculitis decalvans, lichen planopilaris, discoid lupus erythemasus, frontal fibrosing alopecia and keratosis pilaris. Inter- and perifollicular morphology including number of demodex mites, hyperkeratinization, inflammation and vascular morphology could be assessed by RCM and OCT in all included skin disorders. Methodological study quality was low, and interstudy outcome variability was high. Quality assessment showed high or unclear risk of bias in 36 studies. Both RCM and OCT visualize quantitative features as size, shape, content and abnormalities of hair follicles, and have potential to support clinical diagnosis and evaluate treatment effects. However, larger studies with better methodological quality are needed to implement RCM and OCT directly into clinical practice.