The segregated colonies (SCs) in Hungary are populated mainly but not exclusively by Roma. Their health care use is restricted in many respects. It has not been studied yet, whether fair COVID-19 vaccination coverage achieved in Hungary is accompanied with fair effectiveness in SCs. Using census data, the vaccination coverage in SCs and the complementary areas (CAs) in the same settlements of the country was determined. To describe the settlement level differences, the vaccination coverage (until June 30, 2021) in SCs were compared to those in CAs by age, sex, and eligibility for exemption certificate standardized measures. Aggregating settlement level data, the level of geographic discrimination in Hungary was also determined. According to nationwide aggregates, crude vaccination coverage was significantly lower in SCs (40.05%, 95% CI 39.87%-40.23%) than in CAs (65.42%, 95% CI 65.37%-65.46%). The relative standardized vaccination coverage was 0.643 (95% CI 0.639-0.647) in SCs. A total of 437 of the 938 investigated settlements showed significant local vaccination disparities. Hungarian citizens living in SCs, mainly of Roma ethnicity, are a distinct high-risk group. Special intervention adapted to SCs is needed to mitigate inequality in vaccination coverage and further consequences of the pandemic.