Imprinted genes, giving rise to parent-of-origin effects (POEs), have been hypothesised to affect type 1 diabetes (T1D) and rheumatoid arthritis (RA). However, maternal effects may also play a role. By using a mixed model that is able to simultaneously consider all kinds of POEs, the importance of POEs for the development of T1D and RA was investigated in a variance components analysis. The analysis was based on Swedish population-scale pedigree data. With P = 0.18 (T1D) and P = 0.26 (RA) imprinting variances were not significant. Explaining up to 19.00% (± 2.00%) and 15.00% (± 6.00%) of the phenotypic variance, the maternal environmental variance was significant for T1D (P = 1.60 × 10 −24) and for RA (P = 0.02). For the first time, the existence of maternal genetic effects on RA was indicated, contributing up to 16.00% (± 3.00%) of the total variance. Environmental factors such as the social economic index, the number of offspring, birth year as well as their interactions with sex showed large effects. The failure of the immune system to distinguish self from non-self antigens is the basis for autoimmune disorders (AIs) 1. Type I diabetes (T1D) is an AI that causes chronic destruction of pancreatic islet ß-cells and hyperglycemia due to reduced insulin production 2. With the incidence said to be increasing by 3-4% yearly, more than 20 million individuals are estimated to have T1D worldwide 3. Rheumatoid arthritis (RA) is associated with autoantigen presentation with antigen specific T and B cell activation and aberrant inflammatory cytokine production. Consequences thereof include synovitis, proliferation of synovia and cartilage, and subchondral bone destruction 4. The occurrence of RA is relatively constant and ranges between 0.5 and 1.0% in European and North-American populations 5. The exact etiology of T1D and RA remains largely unknown 1 , however, a complex interplay of genetic, environmental, and epigenetic factors is assumed 4,6,7. With regard to genetic factors, the strongest effects have been found within the major histocompatibility complex or human leukocyte antigen system. T1D and RA show genetic overlap in terms of associations within HLA, PTPN22, CTLA4, and TAGAP 8. Causal loci explain over 80% of T1D heritability which reportedly ranges between 40 and 92% 3. For RA, associated variants outside and inside of the major histocompatibility complex region explain about 5% and 60% of the heritability 9,10. Heritability estimates range between 12 and 60% 11-13. As disorder concordance rates in monozygotic twins have been observed to be less than 100%, AIs are assumed to be subject to epigenetic modifications 4,14-16. Perhaps the best-known example for all epigenetic phenomena is imprinting, in which the expression of genes is either maternally or paternally inactivated. Inactivation