Rapid development of analytical techniques in the last few decades has enabled a thorough investigation of the N-glycosylation process in numerous pathophysiological conditions, and the observed changes in many of them have led to a rapid growth of interest in the field of glycobiology. Changes in N-glycosylation are now considered valuable biomarkers of various diseases, and their specificity is being exploited for differential, diagnostic and prognostic purposes. Previous studies have shown that the N-glycan profile of plasma proteins is altered in type 1 diabetes (T1D). One of the more pronounced changes observed was in he abundance of high-mannose glycans in the plasma N-glycome. These structures could predominantly originate from the complement component C3, a glycoprotein with exclusively high-mannose glycans attached to its protein backbone, which is known to contribute to the development of T1D by enhancing autoimmune inflammatory processes. For this reason, a high-throughput method for the site-specific N-glycosylation analysis of human C3 protein was developed in this study using liquid chromatography coupled to a mass spectrometer (LC-MS), based on its enrichment from plasma using lectin affinity matrix. The newly developed method was then used to analyze blood plasma of subjects newly diagnosed with type 1 diabetes and their healthy siblings, and significant changes in C3 N-glycome were observed. T1D was associated with an increase in less processed structures with more mannose subunits at both C3 N-glycosylation sites. Furthermore, C3 N-glycosylation was analyzed in the adult population of T1D subjects with different degrees of the most common complications of T1D – retinopathy and albuminuria. It was shown that C3 N-glycome significantly changes in severe albuminuria in T1D, but is independent of disease duration. Retinopathy led to a change in only one glycoform, while all but one C3 glycopeptide was significantly associated with levels of hemoglobin A1c (HbA1c). The findings presented indicate the involvement of N-glycosylation and the C3 complement component in the pathophysiology of type 1 diabetes and indicate the importance of C3 N-glycome as a potential diagnostic and prognostic biomarker of this disease and its associated complications.