New EU Border System Means Short Flight Connections Risk Missed Flights and High Costs

As travel season peaks, many Israelis flying through Europe face risks with short layovers due to a new EU border control system. Since April 10, 2026, the Entry/Exit System (EES) has been fully operational at Schengen external borders, requiring biometric checks including facial recognition and fingerprints for non-EU travelers. Israeli passengers connecting through Europe usually undergo passport control at their first Schengen airport, even if they do not leave the airport, which can cause delays.

Not all European layovers require passport checks; passengers continuing to non-Schengen countries and staying in international transit zones may avoid them. However, if travelers must collect luggage, recheck bags, change terminals, or enter Schengen territory, they must pass through border control. Recent reports from "Bachadrei Haredim" reveal at least ten Israelis missed connecting flights after allowing only about 90 minutes between flights, due to long queues at border control during peak hours. Presenting boarding passes to border officers does not guarantee priority.

A similar incident occurred last week when a group of Japanese travelers missed a Warsaw-to-Japan flight because their connecting flights were booked separately, forcing them to pay for overnight accommodation. Experts recommend allowing at least three hours for connections requiring border checks, and even more time at large airports or when changing terminals or collecting luggage.

Travelers are also advised to book all flight segments on a single ticket, even if operated by different airlines, to ensure better protection in case of delays. Separate tickets are treated independently, and missed flights may require purchasing new tickets at personal expense. However, even with one ticket, compensation for missed connections caused by border control delays is not guaranteed under EU rules, as eligibility depends on the cause and circumstances. The safest approach is to plan generous connection times and verify transit procedures in advance to avoid costly disruptions.