Spondyloarthritis (SpA) is a chronic inflammatory disorder resulting from a combination of genetic predisposition and environmental factors. Despite recent advances, a substantial fraction of its genetic basis remains poorly understood. Several mechanisms have been proposed to account for this unexplained heritability, including epigenetics which can play a role at the interface between genetic and environmental susceptibility factors. Epigenetics refers to changes in gene expression that are not encoded in the DNA sequence itself. Such mechanisms may include DNA methylation, histone modifications and non-coding RNAs. Disruption of one of these systems can lead to inappropriate gene expression, which in turn might favour the development of disease. Thanks to recent technological progress, there has been a growing interest in the field of epigenetics in complex diseases, including SpA. However, epigenetic studies face some methodological limitations that hamper interpretation of their results: small sample size, absence of biological replication, lack of adequate controls for potential confounders, studies not performed in the most relevant cell/tissues. In the future, integration of epigenetics with other “omics” data will probably be necessary to improve our understanding of SpA pathogenesis. These issues need to be addressed before considering the use of epigenetic marks in clinical routine, as biomarkers or as drug targets.