The crisis in the former Yugoslav Republic of North Macedonia, which began in February 2001 and ended with the Ohrid Agreement of August 2001, resulted in 22 known cases of disappearances and possibly in tens more cases.

In November 2002, ICMP opened an office in Skopje at the invitation of the then President of the Republic, Boris Trajkovski. Although the number of missing persons cases was relatively small, the issue threatened to impede implementation of the Ohrid Agreement since members of the Government at the time of the crisis and members of the former National Liberation Army (NLA) were accused of having been involved in disappearances.

ICMP worked towards the establishment of a transparent, domestic process on the missing, including the establishment of an ad hoc commission to report directly to the Government and the judiciary.

In December 2003, the Government appointed two Coordinators for the Issue of the Missing, to work in conjunction with ICMP and relevant state authorities.  As a consequence, ICMP was able to assist North Macedonia in identifying nine missing persons.

In 2011, the Parliament voted to enforce the 2002 Amnesty Law. Originally enacted in the context of the Ohrid Agreement, the Amnesty Law may be viewed as an effort to support the peace process, but at the expense of judicial retribution. As such, it has had a serious negative impact on efforts to locate persons who have remained missing since the 2001 crisis.