Non-alcoholic fatty liver disease (NAFLD) is an emerging epidemic disease. It represents a large spectrum of liver diseases, and affects both adults and children. The etiology of NAFLD is multifactorial. Indeed, several events such as caloric imbalance including sedentary lifestyle, obesity and/or a predisposing genetic background are key players in the increasing risk for NAFLD development and its progression. Recently, a sequence variation within the gene encoding for patatin-like phospholipase containing 3 (PNPLA3, rs738409) was found to modulate steatosis, inflammation and fibrosis in NAFLD. It was also demonstrated as a novel genetic marker associated with progressive ALD (alcoholic liver disease). In this mini-review, we summarize the current knowledge on (i) PNPLA3 variant(s) in the pathogenesis of liver diseases, and (ii) PNPLA3 gene regulation and potential function in liver.