Intrahepatic cholestasis of pregnancy (ICP) has a multifactorial pathophysiology involving genetic, endocrine, and environmental factors. It is associated with maternal distress and adverse foetal outcomes. The monogenic aetiology of ICP remains unexplored in the Maltese population. We apply whole exome sequencing in 20 unrelated index cases to assess the molecular spectrum of variants in genes linked to bile acid transport. We shortlisted five unique heterozygous variants. Three ABCB4 variants, including a novel likely pathogenic stop-gain variant were detected. Three genealogically unrelated cases carried an ABCB4 p.Asn510Ser variant, suggestive of a founder through shared haplotype analysis. This study provides preliminary insight into the monogenic aetiology of ICP from an unstudied population. It expands the spectrum of genetic variants associated with ICP and provides evidence for a founder effect in the Maltese population.