The rise in divorce rates around Europe has led to an increase in custody cases before national and international courts. In these challenging and often volatile cases, rights of children and parents are simultaneously at stake, rendering decision-making at the courts a highly delicate balancing act. Debates regarding custody policies have been characterized by changing gender roles and a battle for equality, while gender-based parenting roles have become less distinct. This raises questions with regards to the perceived divide between mothers and fathers in family adjudication. The aim of this article is to identify what European human rights law has to say with regards to parental equality in custody disputes, and to what extent it leaves room for parents to be evaluated by different standards. Two main factors are brought forward: contemporary values and perceptions of parenthood, and the indeterminacy of the best interests of the child. The effects of these two factors are analyzed in the context of case law of the European Court of Human Rights and the Court of Justice of the European Union. The article argues that differing evaluation of mothers and fathers in custody-related disputes is, to a certain degree, allowed by the European human rights regime, whenever such difference is deemed justified by the best interests of the child.