Microvascular complications of type 1 diabetes, which primarily include diabetic kidney disease, retinopathy and neuropathy, are characterized by damage to the microvasculature of the kidney, retina and neurons. The pathogenesis of these complications is multifactorial, and several pathways are implicated. These complications are often silent during their early stages, and once symptoms develop, there might be little to be done to cure them. Thus, there is a strong need for novel biomarkers to identify individuals at risk of microvascular complications at an early stage and guide the implementation of new therapeutic options for preventing their development and progression. Recent advancements in proteomics, metabolomics and other ‘omics’ have led to the identification of several potential biomarkers of microvascular complications. However, biomarker discovery has met several challenges and, up to now, there are no new biomarkers which have been implemented into clinical practice. This highlights the need of further work in this area to move towards better diagnostic and prognostic approaches.